http://bitcoin.stackexchange.com/questions/273/how-does-merg...
The actual mining is done by clients using software like cgminer; the pools just coordinate. If the software doesn't support a particular POW algorithm then it would have to be updated and tens of thousands of people would have to install the update. Also, there are pools that auto-switch between different scrypt currencies to mine the most profitable one, but mining software doesn't (currently) auto-switch algorithms.
While this is true for desktop mining and to some extend, gpu mining, largest and most powerful pools use ASIC boxes which are not re-programmable. Some hash algos perform better than others on gpu depending on the parallelization potential.
Ok, so you could theoretically "defend" your new cryptocurrency by basing it on an algorithm that nobody has ASICs for yet, and by the time there are ASICs, its probably defended well enough by mass adoption at that point (otherwise nobody would bother to make an ASIC for it).
Further, just using a new algorithm only protects you briefly, right ? Can't the pools implement new algorithms as they see fit ?