I think Glenn has a little more armor than Maggie because he is so likable and, to a lesser extent, he is one of their very few 'minority' characters (and one of the few east-Asians on TV in general).
If they're smart, and I'm not convinced they are, they have an opportunity here to build them into a healthy and mature relationship that can become the heart of the group. Then, after another season or two of their fight to maintain their love and happiness through the darkness, this lone bright spot can be snuffed out for the most emotional impact.
Alternatively: Kill Maggie at the hands of Merle or someone else from within their group. Glenn turns dark in a very introverted and bitter way rather than the crazy rage that Rick went to. Glenn starts to blame Rick for allowing it to happen. Glenn decides Rick is too dangerous to keep around. Cue subplot of season V.