Oh missed the part about pre-booked seats.
If you booked with anyone other than Air Malta direct (chances are you did) and have been bumped onto the Air Malta flight then all pre-booked seat requests will not be honoured, any monies paid to Thomas Cook, Monarch, etc for exit seats will need to be claimed back on return.
However, once you have been advised by your Tour Operator that your flight as been changed to the Air Malta, by all means give them a call and book your seats, they will only be to happy to oblige. At check in legroom seats are £22 of your hard earned pounds one way, stretch your legs out for 3 hours for the same price of a bottle of wine and a DVD, seems ok to me. Of course pre-booking may be cheaper and usually is.