Well, I'm pretty typically old fashioned in my views on sex, and I do see the virtue in waiting. I do also, however, see Hammy's point, and additionally, marriage would not solve the other issues, nor could it be a guarantee of the underlying cause of the fear being fixed. The chief issue here is the fear of abandonment, which she equates to sex. While there is a valid logical claim in that marriage would absolve the fear of abandonment (you have, theoretically, proven you're not going anywhere by tying the knot), marriage shouldn't be a remedy for a problem like this. It could even, in an albeit extreme scenario, be difficult to ascertain that the reasons behind the marriage are wholly for the right reasons (not to say you would marry her for such a reason OP, not at all. But the point does stand). Marriage should be the pinnacle of the relationship, not a remedy to a relationship issue.

Granted, that does put marriage in the position of being used in a strictly remedial sense, which no one has thus far suggested. But the logic stands for the example.

That all said, the key here is breaking the link between two things: 1) that sex equates to abandonment and emotional turmoil and 2) that she should be afraid of sex on a biological (or perhaps sociological masquerading as biological) basis. Japan is, despite the common internet joke about being the chief exporter of the world's weird stuff, a fairly strict society. It is possible that the pain she felt in the abandonment could play itself into the cultural taboos on the subject.

You're currently, it seems, going about this the best way you can. Do not pressure her into this at all. The issue here on your end shouldn't be about sex, but should be about dispelling the notion that she should be afraid of it on the basis that you're going to up and leave. You can do that without sex itself, and doing so will ease the process on her part. Additionally, don't take her fear as reflective upon you...I don't think she thinks, despite the distances, that you're going to do what her (your word here) of an ex did. You have to understand, the ex was clearly traumatic for her, and trauma doesn't always follow rhyme and reason in these regards. I'm sure she trusts you. She is, in all likelihood, simply unable to disassociate the pain of what she felt from sex. Truthfully, a therapist would be a Godsend in this. You are only able to do so much, though being patient and understanding with her while working through this means more to her than you can know.

As far as you yourself go, there is no shame in being a virgin. There is a great deal of societal pressure, particularly in America, to punch the proverbial "v-card" ASAP, without regard to the gravity of the act. You, I think, are better off for waiting for someone you truly care about to share the moment with. Don't let it get to you...personally, I tend to find societal expectations in regards to virginity to be ridiculous from the start.

Please keep us posted on how things go. I do hope I was of some help.

Hugs,
Harley