I agree with you, but that's not what Bendis seems to be giving us. The version of the Ares/Alex relationship is very different from the one from the Ares mini. Oeming had Ares had express some of the doubts Bendis gave him, but those were specifically related to the fact that Ares was hiding his identity and Alex's true nature from him. Their relationship was otherwise quite open, and I don't see Ares having the same problems now that he and Alex are on the same page.
That being said, I don't have a problem with the idea of their relationship changing after the truth came out, but I haven't seen any indication of that happening. It's a little jarring to go from the mini to this without any transition.