Wasn't the outcome of Outsiders that Indigo managed to reassert herself as the dominant personality, but had the Metamorpho offshoot kill her just to be sure? You'll have to verify that, I haven't read it since, but can't we just say, "Yeah, Indigo is back in charge."?

I mean, we've had villains that lots of people know are villains before and it hasn't got in their way. She's going to have to earn her trust from the non-DC members of the crew just like Luthor anybody else, hero or otherwise would. Her reputation back home shouldn't get in the way of any new nefarious plots she may be concocting, else we're in danger of rehashing a story that's already been written.

But, if the player is really set on Stacy mindwiping people, I don't mind so much. It just leaves Bruce in a, "Oh God, he's going to do something stupid again, isn't he?" situation that I'd rather not hash out again if it can be avoided.