If a Jew is married to a non-Jew and wants to escape the marriage and repent, does the Jewish community (in the United States) provide a sanctuary that will facilitate the escape from the marriage and repentance, as well as further escape to Israel?
Sounds like you have a very complicated situation. This may be a job for a therapist.
Again, concepts of "sanctuary for repentance" don't really fit with the vocabulary of Judaism.
But for theory's sake: at your average Orthodox Union synagogue, if someone shows up and says "I wasn't raised observant, I was previously married to someone not Jewish and now I'm divorced, and I'm looking to increase my level of religious observance", no one is going to bat an eyelash. (Well provided they act like a reasonably likeable human being.) We believe in confession to G-d, not man.
Application for membership to an Orthodox synagogue will involve some checking as to one's Jewish status, and if a member in good standing of an Orthodox Union synagogue chooses to move to Israel, his/her rabbi will likely contact the right people in the Israeli rabbinate (or contact those in America with connections to the Israeli rabbinate) to make sure the proof-of-Jewishness issue is manageable upon making aliyah.
Upon re-reading this question, I realized one other point needs to be covered: even though halacha does not recognize marriage between a Jew and a non-Jew, if a Jewish person is legally married to a non-Jew, then it would be despicable and wrong to just disappear and run away. If their union is over (for whatever reason), then they should go through a civil divorce as amicably as possible.