Tell her "We need to talk." Explain how you feel. That you don't mind giving her advice or lending an ear to her troubles, but antagonizing your beliefs is pushing you away. Tell her gently that if she continues to do so, not only will you be disinclined to help her with her troubles but that you'll go through the proper channels (school administration, teachers, etc.) about the issue. Let her know that you want to be able to coexist with her but that there will come a point where you won't and it could cost her position of Editor.
Now that you've grounded her to reality, ask if these comments she's making has more to do with your history with her than your faith. If it turns out that she's still got some hurt from your breakup, working through that through honest heart to heart discussion should improve things. If not, try to figure out if you're doing or saying anything that would be genuinely offensive to her (being a lesbian she might get a lot of flak from some 'Christians' and may feel that you're like them somehow).
If it is just your belief that she disagrees with, let her know that she's entitled to disagree. But that you're technically coworkers and that there is a certain amount of civility required of your positions. Call truce; no antagonistic statements to each other regarding belief. Whether it is political ideology or spiritualism. Find things that you're comfortable bickering about like Star Wars canon or who would win, cavemen or astronauts,
Most importantly, if she apologizes, forgive her. That's what we're called upon to do.
