Avi K: I don’t know–it’s a hard question, and each BT has to decide what to do in such a situation. Rav Arush’s extensive discussion of such married-to-a-secular-Jew-new-BT-scenarios very strongly argues against divorce, but doesn’t say it’s OK to sin either, so I’m not sure what exact advice he (or other kiruv rabbis) would give in that exact situation. Ultimately the BT will make his own decision.
I agree that’s it’s usually possible to arrange not to have to work on Shabbos and Yom Tov. If not, he should quit and find another job, since most employers out there are more accommodating nowadays.