Of course they do; this follows directly from consequentialism, and is, in fact, an argument that could be used about donating to any charity but the most effective charity. If this was pointed to most people, they wouldn't care and would ignore it or, like the XKCD link, simply indulge themselves that much more.
That's why Folding@home is so interesting as a charity, because while most charities are simply committing sins of omission, Folding@home is committing sins of comission. (You did see the section headers, right? They aren't meaningless.)
Sure, if you assume (as you do) that Folding won't save many lives in the long run, it looks like a bad use of resources if you're purely concerned about charity. But that assumption could be applied to any research that doesn't pay off immediately or with certainty. The LHC uses 180 MW (http://lhc-machine-outreach.web.cern.ch/lhc-machine-outreach/faq/lhc-energy-consumption.htm) for example, or 12x as much as much as your numbers for F@H, and is arguably even less practical, despite no doubt producing many more papers.
Latest in an irregular series, some of whose previous entries were Edge.org and the Girl Scouts...
I examine the Folding@home distributed computing project with reference to the costs (electricity resulting in air pollution causing deaths) and benefits (some papers): http://www.gwern.net/Charity is not about helping. Additional data on either side of the cost-benefit is welcome.
(I also recently split out my essay describing things I have changed my mind on.)