Perhaps you should try and compare costs and benefits more directly?

In particular: how much research can get done by other means for $12 million a year? By paying researchers and technicians, maintaining lab space, etc. For example, MIT spends on the order of $1.2 billion a year on research. How does the contribution of folding@home compare to 1% of the research done at MIT each year? Of course, we'd be buying marginal research, not average research: we can get a good lower bound on the marginal benefit of more money by looking at the value of more equipment or somewhat skilled labor for labs (money that hires additional researchers may just be poaching from other efforts, so it's a little harder to get conservative estimates).

This analysis may be slightly less straightforward, but it gives a much stronger argument against spending power on folding@home. Regardless of how the individual feels about the tradeoff between fundamental progress and lives in the developing world today, they would probably be better served by giving to a charity that does fundamental research.

There is also potentially a large benefit from understanding how efforts like folding@home could be better run. The most conservative estimate for its value would be the marginal benefit of the most effective similar distributed computing project (if the main bottleneck in improving effectiveness was experience with similar distributed computing projects, which may be unlikely).