Sure it can be done. You will need 2 available output channels from the alarm brain(top down, top up), and wire 2 relays to make it work. One channel on your transmitter will put the top down, the second channel will put it back up. Most tops are not automatic, at least not the older cars nowadays, so you may have to keep your transmitter button held down to fully open/close the top. You can also try a window roll up module, like what you would use for your power windows to make them work with the alarm, although I've never dont that before, and dont know how well it could work. I think it may work ok though..

13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
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-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)