Okay. This actually makes a lot more sense than, "Dora is being a crazy, mood-swinging bitch." I'd probably be this insecure too if I thought my boyfriend might still be harboring feelings for his (now our) roommate/best friend that he had a crush on and was rejected by very shortly before taking up with me. I'm not saying she's right, because I think Marten's made it very clear that his attention is square on Dora, but jealousy is rarely rational, and she has, I'm sure, plently niggling at the back of her mind. For instance, Marten would not move out of the apartment with Faye - Dora had to move in. From an outsider perspective, this is a guy not willing to move too fast and leave his comfort zone of 'things as they've always been'. From Dora's perspective, this probably read as, 'Okay, he doesn't want to leave Faye behind.' Faye is treated by Marten similarly to Dora, in that they are capable of having intimate personal conversations. Outsiders would see this as a truly good, supportive friendship. Dora could easily see it as 'treating Faye like me but without the sex.' And the list goes on and on and on.
The fact of the matter is, Dora is right here; not in her perception that Marten was eventually going to leave her due to unresolved feelings for Faye, because I have a feeling that even if Marten does still feel something for Faye, that's not enough to pull him away from Dora, who's he's built this relationship with. No, Dora's right in that if she can't get over her insecurity and get her head back in the game, then yes, they need to break up. It doesn't have to be permanent, but that's up to her and her ability to overcome her security issues. At the end of the day she's the only one who can learn to get over this; no one, especially not a boyfriend, can teach her to love herself. That's what the real issue here is - self esteem, leading to insecurity and jealousy.
Say what you will about Dora following past M.O.s of getting out before things have a chance to blossom, but I think her reasoning here is sound (which is probably why Marten has that devastated silence for two panels - not only did she just dump him, but it's difficult to argue with her logic because it's not about his feelings for Faye but how Dora perceives them, which is something he cannot change). I'm just hoping she doesn't actually burn this bridge she's crossed after the fact.