An organization is ill if it tolerates its employees having differing political and/or ideological beliefs?

These are not organisations that have individual employees who, on their own time, support SOPA. This is organisations that's policy is to support SOPA.

That's not what is at play here. "The company" is the one supporting SOPA, and "the company" is sending representatives to YC demo day.

It doesn't sound like you would be banned for merely working for the company and being interested in YC - it's keeping that company out of the process.

That's a little naïve.

Maybe, but why take the risk?