hi! You don't need to answer this (unless you want to), but I just got halfway through ch. 3 of the golden heart au and I have a guess for what happened.
Leon mentioned a 'him' but neither monokuma nor Junko have been seen yet. Leon's 'name' (11307) has been painted everywhere, though. On the other hand, Leon seems wholeheartedly intent on protecting the 'innocents', no matter what. This could be a fatal flaw, but to me, this also points to his innocence.
So what happened could be:
A) Junko's quirk is shape shifting, and she murdered sayaka disguised as Leon, during which the actual Leon walks in - which would lead him to think the shape shifter is a guy, and Sayaka's blame being pinned on him. Or,
B) Junko disguised herself as Sayaka and attempted to kill Leon, leading Leon to kill Sayaka after which she disguises herself as (my initial thought was Monokuma, but Naegi seems a bit more likely,) to taunt him about killing someone innocent. This could add reason to why Leon was so certain why Naegi was guilty, only 'easing' when it turned out Naegi has a different quirk. 'easing' in quotations as he doesn't seem to think Naegi is the one who did it anymore, but still thinks he's in cahoots with the person who did.
Sorry for the rambly ask, just had to get my thoughts out somewhere, and didn't want to give anyone spoilers Incase I'm right.