I really doubt that MS will issue a FW update, some flashes will go wrong and this will result in bad publicity. For this same reason (bad publicity) and legal issues, I REALLY doubt they will try to do damage to any hacked 360 on LIVE. But of course, like said before in this thread, all we can do at this point is speculate.
However, I think they will just issue a kernel update. There are a LOT of ways to detect this hack. People are talking about checksum checks on the FW, but I doubt that MS will even check the FW. I think they will check the DVD-ROM in the drive instead. Currently, the 360 will boot your backup, but this doesn't mean that your backup is exactly the same as the original. In fact, there are a LOT of differences between your backup and the original. So, I'm guessing that MS will just read some stuff from the DVD that won't be on your backup and if the stuff is missing, the 360 just won't boot the disc.