@Syanalassa Pretty much all of that is covered in chapter 2 and while it's not included in the manga adaptation, Makoto himself says via internal monologue that Maka pretty much cleared up almost all of his doubts right before he escorts her to the train station after R-15 video incident.
And really, the SID girls would've done the exact same thing to him(ignoring his feelings and forcing what they want on him), only that the very rules of SID prevent that from happening and them from making a move until Maka forced their hand.