Have you actually read any of the blogs that left?
Yes, I have. If you're aware of one which isn't a variation on "blogging alongside these corporate cola shills will tarnish my reputation," I'll be happy to read a couple more.
Dude you have no idea how reality works now does it.... One of the bloggers that is contemplating leaving had an attempt on his job because of a conflict of interest that didn't exisist. People are that dam paranoid and any sense of impropriety will be latched onto and used to descredit someone.
I'm not sure I'm understanding what point you're trying to make here, but I'll tell you how I think the reality of this situation works:
The exodus of people who object to having paid corporate advertorials share their space will make the environment at the site more accepting of having paid corporate advertorials share the space. After all, the people who object will be gone.
Science bloggers will still be elbowing each other aside for a chance to write on Scienceblogs. If their writing is high-caliber (and why shouldn't it be?), the reputation of those who remain will not suffer, any more than the reputation of NPR suffers for being sponsored by AG Edwards or similar.
If PZ One-note leaves, his band of angry atheists may have to find someplace else to vent spleen, and traffic at Scienceblogs may initially drop by half. Its reputation going forward will be determined not by those who left, but by those who remain and those who come onboard subsequently.
If the editorial content is high, and the barriers to advertising are low, the site has the potential to become not only educationally but financially successful.