1. Yes. If you rent out within the first two years of ownership, you become liable for stamp duty.
2. Other than not renting it out, not that I'm aware of.
Depending on your circumstances, and whether or not you have any cash reserves to fund the mortgage for the time being, you may be better either (a) selling for whatever you can get [though depending on where it is, there may just be no buyers at all], or (b) holding on to it for another few months and at least not renting it out until after the two-year mark.
In any case, since it's no longer your PPR you should stop claiming TRS. I'm not sure what the stamp duty implications of this are, actually - if it's not your PPR within 2 years there could be issues. Anyone know?
There's another option - depending on combined circumstances, it might well be more tax efficient to move into your apartment for a few months and rent out your wife's house for six to nine months.
Good luck. You'll probably have some tough decisions no matter what you do. Hope it works out well for you.
[and congratulations!].