rabbitoid: The solution is very simple - the site shouldn't set the timeout of games according to vacation days like now but according to their original time settings (much simpler too).

So, if you have the next month set as vacation days and your opponent moves on a 3 days per move game, the deadline would still be set as in 3 days for now (instead of in 1 month as it is now). However, in 3 days from now, when the game was about to timeout, the system would notice that it was a day marked as vacation day and add another 24 hours (this is already working like this now, I think). And it would keep doing that until either a non-vacation day was reached (timeout) or you moved (business as usual).
Naturally, you shouldn't be able to mark the current day as a vacation day (which you can't already).

So, the site already has everything it needs to fight this problem. This would be one of those rare events where to solve it, all it takes is actually de-implementing something