Of course if the bfl Asic became too much of a problem one could modify bitcoin protocol just enough so that the ASIC doesn't work or is severely hampered. They are very specific. A fpga can be reprogrammed. An ASIC would be nothing more than a coffee warmer then, literally.
Why are some people seemingly under the impression that ASICs are 'evil' or 'a problem'? ASICs are not the boogeyman. They will be used for mining, just like FPGAs are this year, just like GPUs were last year, and just like CPUs were 2 years ago.
They are a natural evolution of an efficient solution for the proof-of-work problem that the bitcoin protocol presents. The fact that someone has the cajones to dump serious capital into development of something like this is evidence that bitcoin is thriving, in fact, growing. This is a good thing for all of us.
Yes, the large-scale deployment of ASICs will make GPU (and to a lesser extent, FPGA) mining obsolete. It will drive difficulty up to levels never seen before. That is, mining with GPUs and FPGAs will no longer be profitable. So what? Just like the arrival of GPU mining en-mass heralded the demise of CPU miners. So what? We either chose to embrace ASICs as miners, or we take our profits and GTFO of the mining scene.
What may happen is that when ASICs are deployed en-mass, the 'average miner' will have a farm that has 20x the hashrate of what they currently have. So instead of a 5Ghps miner being the 'average', it will be a 100Ghps miner. If that miner has $4k worth of GPU/FPGAs now, he can choose to 'upgrade' and buy $4k worth of ASICs. The difficulty will be 20x what it is now, so 30M instead of 1.5M. Bitcoins will still be $6 (they will still be generated at the same rate so supply remains the same).
And this all means that mining profits for the previously mentioned 'average miner' with $4k worth of 100Ghps ASICs will remain the same as they are now. If he is making 3BTC a day with his $4k 5Ghps rig now, he will continue to make 3BTC a day with his $4k 100Ghps ASIC rig. Nothing changes.
This is 'evil' or 'a problem' how? It is only a problem for those who are currently invested in GPUs and FPGAs and who don't want to change. Change or die. That's how it's always been. It was the case with the CPU-to-GPU transition, and we are seeing the beginnings of it now with the GPU-to-FPGA transistion, and we have already been warned that an FPGA-to-ASIC transition is looming. No one is forcing us to continue mining, but many of us will.