Not sure if it's in the rules, but I would never let an AMF stop an Epic spell, chalking it up to the line about "mortal magic." If we're talking about wish/miracle, it's possible the caster might also be epic.
Like others, I'd allow wish/miracle to destroy an AMF, but that's not RAW.
Note what is RAW: Iron Heart Surge, a level 3 maneuver, can literally punch an AMF down. I don't think it's out of line to let a wish or miracle duplicate the effects of such a low level martial maneuver, assuming it's cast from outside the AMF.
I don't think that works....
Is Iron Heart Surge from Tome of Battle? I guess I should have had her cast an immediate action spell to move out of the way when she got debuffed. I haven't really used the book before in this campaign...
It's 20-20 hindsight now. However, if they try that again, I'd hopefully be a bit more prepared for it, as my BBEG is smarter than me.