I think it does disable the controller, unfortunately. I have a Rev. A or B model iMac, and I tried this, and it wouldn't work. Evidently, this particular iMac has been updated (I've never bothered to confirm that, however).
Eventually, maybe dougg3's ROM/Firmware hacking technique can be used to circumvent this issue. His G3 firmware project could be adapted to an iMac, probably.
I'm a little curious, If you need to update the firmware to run Mac OS X (which, by the way, doesn't recognize the old floppy drive anyway), does the update serve any other useful purposes, such as bug fixes and the like? It's conceivable that the iMac would function just fine without this update under classic Mac OS, if all it does is provide Mac OS X compatibility.
Who knows?
c