I don't think folks have to avoid MD5 as strongly & immediately as you suggest... the attacks are for the most part theoretical or require more compute power / patience that people outside of this blackhat con can muster. It was my understanding the PS3 cluster actually got a cert which could be used nefariously... and this guy showed he could do it cheaper and faster. This is perfectly inline with my understanding: Attacks always get better, they never get worse. So I suppose it is time to work out a migration plan for whatever uses MD5
On your closing comment: I think the author was suggesting that if people had been paying attention a lot more of them would be using ATI GPGPU clusters for stuff they used to use Vector processors and now use fleets of X86 variants for.
I don't completely disagree with him but there a lot of small GPU clusters out there and there are a lot of reasons why more people haven't really got with the program. I think the biggest reason is the difficulty developing for GPGPUs. It's not the hardest thing I've ever done but it really takes a deliberate effort to get into a different state of mind. And the ATI SDK just plain sucks. I'll take the performance hit and develop using a C superset with a NVIDIA target. The process can run during that extra time I am not pounding my head against a hard flat surface. Actually now that I think of it, I've just kept a lot the old FORTRAN code I have and used the NVIDIA kit... rather than porting to the ATI SDK.
Having said that I don't think that this state will last long at all. The rate of increase of performance in GPUs is steeper than that of CPUs; AMD & NVIDIA are really serious about getting into the general compute market (with the same or similar chips to what they already market); The power consumption, cooling, and noise are all really favorable.
I am sort of curious what OpenCL will be like, being a Mac user... but here lately Apple has been going further out of their way to make things suck, so I am not holding my breath.