Well, okay, it's not as simple as abandonment issues. The breaking point was probably Siam's words. We know they had been separated for a long time until they met again at the train. She was already working for the snakes at that point and I guess she figured it'd be "no hard feelings" but his last words kinda lingered. As for why he said that we may never know :V
Why did she turn on Siam? People say it is jeleousy but I think there is more to it than that it is just that the authors didn't explain it well enough. They didn't even give a reason why Alphard turn to the Dark side.