Pure speculation on my part, I dont know too much of the overall scope of the hack (besides what I read online, which I will take as potential truth at best), but I think best bet to contain the hacks will be to do online checks against online services. Even doing a MD5 hash checksum on the running firmware will pretty quickly let Sony know if the MD5 hash matches the original hash they released. Anything that does not match could be considered altered/custom. I would imagine it would be difficult to mimic a MD5 hash.
Of course this is only for devices that connect to the internet. Im sure its possible to disable checks, fake DNS entries, submit fake info, but that would most likely eliminate you from using online services.
The most likely scenario will be that this will turn into a game of cat and mouse (aka damage control). In order to use CFW, you will either need to forego online services or jump through hoops. Best case for Sony would be that if you create enough hoops often enough, you will curtail your CFW population. Like everyone has said prior, every system has some subset of its marketshare that have compromised the console.
The situation sucks for publishers and development houses. Sony will take some heat from each, but will probably sell more gear. This would be something I would go after if I was 13 again. I can pay for my games and want to reward developers for jobs well done. As for homebrew, I modded my old original Xbox and wanted to check out XBMC. It was cool in practice, I just never really used it.