I guess my question is, did leaving the battery connected during the unplugging of the original electric fan clutch result in damaging the ECM?
I doubt it very much. When the engine is off, power to the fan is cut off.
Dealer is trying to fleece you into buying a PCM with the usual sticker shock price (let me guess, around $1000?). They're idiots.
What is the code you're getting? I'm guessing it's a wiring issue or it's not plugged in right. Double checking costs nothing.