Real Genius/WMG

Mitch, Chris, and Lazlo are a gender-reversed version of The Hecate Sisters.
Mitch is the maiden: he's innocent and responsible for initial inspiration. Chris is the mother: he creates things and plays a nurturing role. Lazlo is the crone: mystical and vaguely disgusting. Also, they seem to be in some sense the same person: note Chris's comment to Mitch that "I used to be you," as well as the way Sherry confuses Mitch and Lazlo.

They did something to the popcorn besides shoot it with a laser to get it to rupture the house.
Genetically altered superpopcorn? Maybe it wasn't real popcorn at all, but super-expansive foam kernels with greater force and resilience to crushing force than mere Zea mays averta. The science group may even have weakened the roof and wall seams of the house just to get the desired effect. Just because Myth Busters busted the details shown on screen, doesn't mean there couldn't be an unseen explanation!
 * If you recall, Ick had shown off genetically engineered jumbo cherries earlier in the film. Not too much of a stretch to believe that he came up with a super breed of popcorn and maybe worked with Jordan to make the optimal giant Jiffy Pop tin.
 * Concurrently, upon learning about Hathaway's aversion to popcorn, Chris had Ick create a super breed of popcorn for use in a (possible) small scale prank, and later decided to one-up the prank upon learning of Hathaway's treachery.

It was an Esoteric Happy Ending.
Hathaway's weapon worked. Blowing up Hathaway's house still proved that it worked; and it's shown that the CIA knew it was a problem with targeting; not the laser function. Chris had given the schematics (the dynamite laser) to Hathaway before he decided against it. Even if the original Kill Sat was destroyed after destroying Hathaway's house due to the reflected laser; Hathaway and his military contacts would have made copies of this information. The kids notifying the Dean and a Congressman simply meant that there was evidence that they were working against National Security. The CIA got other Kill Sats created; and the kids got expelled and/or arrested.
 * Arrested for what? There is no physical evidence of their break-in, and the only thing the Congressman can testify to is that some stranger asked him to meet Dr. Meredith at Professor Hathaway's house the same day it got melted by a giant 'weapons malfunction'. The only person who could possibly finger the kids is Dr. Meredith, and he has no reason to do that because he likes Chris, shares many of his attitudes, and Professor Hathaway was ultimately screwing Dr. Meredith over too.
 * Also, the only thing the Congressman had been told was that he was needed for a discussion with Dr. Meredith on something of 'critical international importance', and that the evidence was at Hathaway's house. Since that statement is literally true - the dynamite laser is such a matter, and the evidence of its existence is indeed inside Hathaway's house in the form of Hathaway's lab notes and paperwork - there is plausible deniability on the part of whatever mysterious parties decoyed the Congressman there that they had any foreknowledge of an incoming laser beam.
 * Likewise, the fact that the kids knew about the existence of the secret project cannot be used as evidence against them. Of course they knew about it -- they were the people who'd originally invented it, at the project director's own request!
 * tldr; While the kids are certainly suspects, there is nowhere near enough evidence to actually make a conviction stick beyond reasonable doubt, and given the major egg on face the laser project has already there are vanishingly small odds that they will want to make a federal case out of it. This would of course change and the government would want their skulls on pikes if they ever found out that they'd deliberately sabotaged the project... but the protagonists left behind no evidence pointing to them, and it is arguable if the government will even suspect sabotage.

It was a straightforward Happy Ending.
People saw the laser fire, and one of those people was a congressman. The news media would have been attracted to a story about a house cracking open after being filled with popcorn, and eventually more facts will emerge. Thanks to this the use of a laser will be subjected to public scrutiny. Congress will hold hearings on the ethical ramifications of the usage of such devices, and at worst the project will be buried under red tape. And thanks to The Great Politics Mess-Up, the laser project won't see the light of day thanks to the end of the Cold War and the collapse of Soviet communism. Even after all that, too, the military will be hesitant to use a potentially unstable laser system. They likely do not know about Chris and Mitch's tampering--all they saw was a laser miss its target and go kablooey.

As for Chris, Mitch, and company: at worst they get a slap on the wrist for breaking into Hathaway's house. Kent becomes a more spiritual person and mellows out, thanks to his encounter with "Jesus." Chris graduates with Dr. Meredith's blessing and gets the Darlington job; Mitch graduates a few years later.

Hathaway is just about the only person who doesn't get a happy ending. He doesn't have a house, and the government audits him for the money that was spent on the laser project (which, if you recall, he instead embezzled to fix up his house). He probably will also be brought before a board at Pacific Tech, and will lose his tenure and his job.
 * Caveat: the accident investigation team taking the laser apart to try and find out why it fired off-course and then melted will find the traces of grease on the lens, which will tell them why it melted. They likely won't find the cause of the firing off-course, but since there is no hardware fault for them to find (as it was a deliberate software error introduced by the chip switching), the most probable conclusion for them to reach is the true one; that the targeting failure was the fault of the software. Whether or not they suspect deliberate sabotage or merely the black swan event of a thumb-fingered mechanic who didn't clean the lens after installing it happening on the same day as a major software bug, either way they will rationally conclude that there that the cause of the incident was due to mechanical fault, not inherently flawed design. And given that the dynamite laser clearly does work in one significant aspect (the laser beam actually is as powerful as advertised), the rational conclusion for DARPA to reach is that its worth at least some more money to put into future testing to try and work out the bugs.
 * Especially since the project has already succeeded in achieving the desired theoretical breakthrough; getting 5+ megawatt bursts of power out of a laser in readily weaponizable form. At this point the only thing left is to perfect the targeting system, and that's the easy part. Aiming a speed-of-light line-of-sight weapon is a mathematical and engineering problem an order of magnitude simpler than trying to, oh, hit an incoming anti-ship missile with a 20mm cannon shell in mid-air with virtually zero time to aim -- and that's a job the Phalanx mount on any US Navy warship has been able to do for the past 30 years.
 * There is also that they have at least one successful static test result (the lab firing) to tell them that the beam comes straight out of the business end, meaning that they know if the beam went off-course its because the laser was pointed the wrong way -- not because the things shoots beams randomly sideways.