Bottom line - if she believes in Christ, then she's Christian, not Jewish. Period. That is the firm, non-negotiable dividing line between Judaism and Christianity -- do you believe in Jesus as the Messiah/Savior, or not? If you do, then you are a CHRISTIAN, if you don't, then you are a JEW.
The whole "Jews for Jesus"/"Messianic Judaism" thing was started in the 1940's by a Southern Baptist Minister as a sneaky, underhanded way to convert ignorant secular Jews who didn't know very much about their own religion to Christianity, by presenting it as just another "denomination" of Judaism. Its NOT.
So if she's a Christian and you're a Christian, you should be fine together.