To answer your question, yes you can disconnect the alarm module without effecting anything else.
( you have to remove the wiper arms and the plastic cowling to get to it however )

HOWEVER ! I have never heard of the alarm module causing the lights to flash, it only has 3 wires running to it :
1. a ground wire
2. a 12v always hot wire.
3. a signal wire that tells it to holler.

I would suspect the CLPM in the trunk as the culprit ( along with 180 ),
might try just disconnecting the 3 electrical plugs to it, spray all with contact cleaner,
let it dry then reconnect.