Morty wan't a genius like his grandpa Rick was. Even Summer and their mom Beth were smarter than him, and even if he was smarter than his dad Jerry, that didn't amount to anything.
But, stupid as he knew he was, Morty was still able to value the nuances and complexities and emotions of life- whether it be human or alien- and that, he'd come to realize, was more than he could say for Rick and, to an extent, Summer.
When he was with Rick, in a life or death situation (which summed up most if not all of their adventures) he found it was easiest to not think about whatever alien force was trying to kill them and instead just focus on survival. Focus on the consequences that would face him and Rick if he didn't do something.
This was harder to do when they were facing an armada of Galactic Federation aliens, who were mostly just following orders and who probably hadn't even done anything wrong. With King Jellybean, it was easier, because he was in the process of doing wrong, of molesting him for no discernable reason other than for his sick pleasure.
But that still didn't mean Morty wanted him to die- just to stop what he was doing and maybe change into a better person. But as Rick had explained to him when he came back from killing the jellybean( and Morty knew Rick did it for his sake, even if he didn't say anything), beings like that, who get off on causing pain, don't change, and if they do, it's only because of an irrational fear of death and the belief in eternal punishment for their crimes.
It didn't make it any easier to deal with afterwards, though. Maybe in the heat of the moment, when it was kill or be killed, Morty could kill half an army to keep his family safe as they killed the other half, but afterwards? When it was three a.m. on a school night and he'd been lying awake for the last five hours, and would still be awake for the next three until his alarm clock went off? When he couldn't fall asleep and stay asleep without some sort of nightmare waking him up every few hours?
It wasn't like he could go to anyone for help, either.
His mom would never understand; she knew Rick took him out on interdimensional adventures all the time, and that somehow her father had a history with the Galactic Federation, but she wouldn't be able to cope with the knowledge that her son- her sweet idiot son- was a murderer, no matter how much he regretted it.
And Rick himself, who was responsible for Morty's anguish, was hardly any better, because while he'd definitely understand, he was a man of science- of logic and equations- and science had no room for emotional conflicts.
When he killed King Jellybean, that was vengeance for his grandson, but it wasn't the emotional comfort Morty had been wanting.
Even when he'd turned himself in to the Galactic Federation and allowed the family to return to a normal life (or as normal as it could've been at the time), that was just a small part in a plot to take the government down and regain power as the head of the family.
And then there was Summer.
In a lot of ways, she was more like Rick than anyone else in the family. She was smart, and cared just as little about emotions as he did. When they wound up in that post-apocalyptic dimension, she was just as excited to beat up as many people as she could as Rick was anxious to get his stupid shiny rock, and as Morty was eager to get home.
Maybe dad would've been able to provide comfort, but he wasn't there- and probably never would be again if Rick had his way (and he most certainly would if mom's abandonment issues had anything to say about it). And even if he was there, he'd spend a lot of time yelling at Morty and making him feel even worse than he already did about his actions.
So in the end, Morty would be left to deal with it alone. But that was fine.
He didn't need to rely on others for everything all the time.
