Actually, there are two problems:
1) End of 3-months movement, and
2) Bug where factors/corps are repatriated from a ceded province the current player owns
For the bug (# 2), send them to the person's home nation or something. But, fix the bug, too, so it no longer happens. People should be able to garrison their own property.
For the end of 3 free months worth of movement (#1), yes, vaporize them. If the owner couldn't pick them up in time, that's his problem. However, for this to work, he may have to move something IN to the territory (a corps to pick up the factors), so make sure that's allowed. Alternately, all the owner to place a corps with garrison factors as if it were his home nation (for the 3 months only). These could be very difficult to code.
So, before implementing "vaporize them" (for problem number 1, now), make sure all potential avenues properly exist to get them out.
NOTE: It is entirely possible that a person cannot move out in time with only three months. The original rules basically said you had to move them out by the most direct route. There was no time limit. For a war against Russia, for instance, France can easily require more than 3 months to get them home. If at war with GB, he may have to march them overland, even if they originally squeezed in from sea.
So, as a compromize, using "3 months, then repatriate randomly" is reasonable (I think this is the way you currently do it).
At LAST! The greatest campaign board game of all time is finally available for the PC. Can my old heart stand the strain?