hi dgaines,
well if the transmitter is housed in a usual metal case and the coax cable going off to the antenna is ok then the radiated RF from the transmitter and coax will be negligible. 99% of the RF will be transmitted from the antenna and as you said its quite some distance away. over 50ft of coax, with 5W going in, there's (without doing the exact attenuation calc's) probably only ~ 2.5 - 3W at the antenna anyway.
Thats a pretty low power level. Have you a mate in the radio electronics trade that has a spectrum analyser ? (if I lived near you I would pop around with mine) that would conclusively tell you what sort of RF levels were present in the room with fire control gear. There is the possibility there is some RF being picked up by the fire control cabling from throughout the building. BUT flamin' heck if they were having probs with a 3 Watt radiating antenna >50ft away then the systen is going to totally fall over with every security guy and other bloke with a 3W handheld radio rigtht up close and personal with the gear!!!
As jackoroko said.... I would almost be tempted to switch back on without anyone knowing and see what happens ... specially now whilst things are under construction .
cheers
Dave