you can definitely do it with an aftermarket alarm or starter, but you should be able to do it with the factory key fob if you make the trigger the lock/unlock buttons. only problem with that is, is that they will probably roll up or down when you hit the lock or unlock button in the car too.
I've done this in my car, but using a compustar alarm/starter. its not all that difficult, you need 2 relays per window, so doing 2 windows and the sunroof = 6 relays. it has to have a timed pulse (mine are 5 second roll down and 10 second roll up) and this is where the aftermarket unit comes in. its possible without still if you use a timed relay that you can set, but I can see that getting expensive.
if anyone wants more info on connecting to an aftermarket unit, I can help, or I can try to help out with OEM integration