Moral Orel/WMG

Clay did actually love Orel
It's just that he was too insane to act upon it.

Orel was an angel.
He however cant remember it. Orel the angel screwed up royally and got punished by god with being reborn as a mere mortal. He loves to go to church because it's the only way he can be closest to heaven and god. It's also why in episode "Grounded" Orel even after several electroshocks comes back to the living world. God didn't want him back.

Angela's death is her Thanatos Gambit.
She knew that it is end of her life now that her heart is weak due from too much alcohol and smoking. That's why she allowed Clay to see the photos of his unborn siblings, and uses his fake suicide to kill herself.

Clay is The Antichrist.
He goes into trouble from the moment he killed his own mother by his fake death to insulting his father so that he can be slapped. What else is that he shot his own son, Orel, so that he can hate him. All of Moralton hates Clay because he will cause the end of the world with his beliefs.

Orel has been in coma all along in season 3.
The episode "Grounded" takes place before "Nature part 1", right? Therefore, the events of Clay shooting him and the rest of season 3 happens to be a dream.

Orel would have had a worse adolescence and adulthood if the show continued
As is stated both here on the main article and on That Other Wiki Moral Oral's happy ending was the product of a forced Gecko Ending by the Executives of Adult Swim. So It can be assumed that if Moral Oral was allowed to continue for a possible 4th and 5th season Oral's remaining childhood would have gotten increasingly worse.

Since the Deconstructionist humor was on what seemed to be a increasing Slippery Slope along the Sliding Scale of Idealism Versus Cynicism regardless of what Word of God had said about Oral getting darker and yet growing as a person. Nothing would stop Orals creator from making things more and more miserable for his lead character and his universe. If oral didnt become just like his father the viewers would have either seen Oral become a miserable homeless drunken strung out wreck or some Evangelion type Fate Worse Than Death like some paranormal force of wrath or brutal justice killing everyone in town leaving only Oral alive a hollow insane shell.

Clay Puppington is the Big Bad of the entire series all along, not Ms. Censordoll.
Maybe she's just a scapegoat to confuse the audience. He even allowed her to control him into shooting Orel and losing respect for him as his plan. Remember the part where she tried to become the new Mayor? It turns out he planned it confuse Orel. When she quits, she just did it so that Clay would keep his position as Big Bad.

The Big Bad is Satan.
Isn't Satan the Big Bad of all of Christianity?

Everyone is The Antichrist except for Orel.
And even the people who are nice to him.

Clay has a Split Personality.
He created a good personality to dissociate himself from the childhood he has. This personality is shown in "Help", but the original personality took over when Clay is introduced to alcoholism. After Bloberta punches him, the good personality takes over again to marry her, but the bad personality takes over the time after the marriage. When Orel is born, the good personality took over this time to teach him the bad things he has done. However, it comes to an end in "Nature" part 1 and 2 when Clay drinks too much alcohol that would result in the original personality to become dominant permanently.

Oral and his brother(s) were put into foster care after the events of "Nature"
Shapey and/or Blocky's bizarre behavior got the attention of child protective services who sent over a social worker to investigate. After Oral told the social worker about his hunting trip with his Dad, the Puppingtons soon lost custody and the boys were put with a more competent foster family. That's why adult Oral is so well adjusted.

Clay orchestrated Orel to hate him for a reason.

 * Yes, precisely so that Orel would grow up to be just like him. And that's no WMG, it's pretty much canon.
 * while Clay did make his son hate him it's for Oral to hate him so much he would always fight back giving Clay the abuse indused attention he wants.

Oral and his brother(s) will be taken by Child Protective Service after the series finaly and adopted by Stephanie and her father
When Stephanie finaly hears what happens at his house (proably from Orel at work), she called CPS who then sent over a social worker to investigate. After Oral told the social worker about his hunting trip with his Dad, the Puppingtons soon lost custody and the boys were adopted by the closest thing to a loving/competent adult. That's why adult Oral is so well adjusted.