One is that the "mask" can be a Christian one. Someone who thinks they are doing the right thing and simply "going through the motions" as it were, but undernieth is just another shlub looking to get some attention (Ironman really is a great example here).
Two is, as you touch on in your post, that the X-Men are very much the big exception here. They try to do good in a world that would for the most part like to see them all dead, all th ewhile holding onto the "not sinking to their level" ideal longer than possibly any hero in Marvel.
The X-Men also have the greatest example of Christianity in modern pop-culture. Nightcrawler (my all time favorite charecter) has been ordained in the comic, has wrestled with real Christian principles (witnessing to both co-charecters AND readers alike), and stood by his faith in th emost dificult of situations.

If ever there was a Christian roll modle to be found in comic books, it’s Marvel’s own Nightcrawler!