Yes, the alarm will go off. Before disconnecting the battery, the alarm must be disarmed.
1. With the fob with you, turn the ignition on
2. When the alarm has disarmed, pull the main fuse of the bike.
3. Once the fuse has been removed you can disconnect the battery
Bone Doc is correct. I had to do the same thing. After not understanding at first. I disconnected battery, alarm started screeching. Put it back on, turned on accessory switch, then pulled battery connections, no problem. Good setup, really, to keep someone just cutting the battery wires to disable the alarm before stealing.