Having Mags as a good guy was never going to stick, anyway. The X-Men need a killer, A-List villain, and none of the others quite match up, in terms of renown or their level of power. Therefore, you have something like Eve of Destruction, whereby Mags goes ridiculously over-the-top in making his point and being a nasty bastard to Charles (and his treatment of the Professor here is probably only slightly less worse than the bullshit we got in the Ultimate Universe)...
On another note, whatever happened to Lenil Francis Yu? He used to be this good, Eve of Destruction and his earlier revamping of some of the X-Costumes were stellar. As soon as he did Superman: Birthright, though, everything went down the pan.