I won't say this makes sense but i can somewhat make some guess work on why ScottandStiles were so easily pushed into Scott and Stiles.
Scott has previously expressed, while under the influence of Motel Hi-jinks, that he considers pre-series Batman and Robin to have been a pair of nobodies and would rather be dead than return to that "baseless" existence.
Fast forward to present events-he's losing that Alpha wolf edge and slipping back into asthma ridden loser McCall.
Scott's head space-he's feeling pretty vulnerable and doubting himself as a sound leader. Now the only feasible reason I can cook up as to why Scott was so willing to at least begin to doubt Stiles has to do with the "I can't trust anyone because you trust everyone!" revelation a few episodes ago. Scott has a fairly fresh example of Stiles admitting that he does not trust Scott's judgement (as far as how to deal with the "bad guys" anyway) as well as a display of some pretty aggressive behavior, stemming from his frustration with the situation, towards Scott's "Superman Syndrome". Although he at first finds it hard to believe and even maintains that it is, "impossible/not possible", he quickly reviews recent Stiles behavior v. Stiles he's known since toddler hood behavior and admits that the IDEA of Stiles losing control and going vigilante on the pack is not as far fetched as he'd like to believe.
IMO, that's why he doesn't immediately bust out with the whole, "Theo told me blah blah blah...", because while he wants to believe it's not true he's very aware that Stiles, even before werewolves became more than just a fairy tale for them, has always lived in the Grey of right and wrong. It's not a hard stretch for him to believe that Stiles, with the stress of a previously coyote girlfriend, Nogitsune detailed baggage, and dying kids galore, might exact his own version of justice.
I also think its supposed to tie in with his feelings of helplessness over the Dread Doctors. Kira has just skipped town with her family-a situation that he in all his Alpha greatness could not fix, several children have died on-in his mind-his" watch, his baby Beta no longer believes in him (that's like Bambi flipping his tail up at his Father), Deaton has gone AWOL, and again Stiles has also admitted that he believes Scott is too trusting to be objective.
Unfortunately the only person who hasn't criticized Scott is our resident baddie Theo who just so happens to be showing up Scott in the reliability department. I think Scott has taken all the shots to his credibility as well as his sudden loss of an indestructible body (basically his confidence) and turned it into a desperate, "I need to better-I have to!" mentality. Which would sort of explain his rough behavior with Corey-he didn't want to let another person down and was again guiltily disappointed that Theo was the hero in the end.
So when Theo expresses his belief that Stiles has turned into head bashing psychopath, Scott inadvertently becomes the Stiles of their relationship and he actually can't bring himself to trust that Stiles would only kill in self defense because of the lack of direction he's been in recently/ as well as the doubt he now holds in his own "too trusting" hands. Scott just so desperately doesn't want to make the wrong choice by believing in something he shouldn't have.
Ironic I guess?
For Stiles, I can only say it must have been a combination of "I knew I would lose him" and his own guilt. He clearly believes that Scott is a better person than he is so I'm guessing he thought if Scott, who never blamed him for the Nogitsune incident and always understood his less than lawful behavior pre-series, could tell him what he did was "right" then maybe he could forgive himself. So to have Scott, who was willing to give creepy Theo a chance, confess that he couldn't completely believe that Stiles killed Donovan in self defense was devastating.
When even his human moral compass was at a loss at what to say it just sort of broke his heart.
The way it was set up was BAD though. (I still can't really wrap my head around why Stiles kept insisting that Donovan was going to kill his Dad...he was already trying to kill you!)