Just so you're aware, the JoS/SO/ServerFault job boards do not even have a concept of applying via the website. The idea here is to reach the crowds that are on StackOverflow and ServerFault--not to force you to expose your profile in your résumé. Doing so is entirely up to you. Don't like your profile? Don't mention it in your cover or résumé. Simple as that. The résumés are always cross-listed, so there's no way for your employer to even know that you necessarily saw the post on SO instead of Joel on Software.
All that said: admitting I might be atypical, if you gave me your SO profile, I'd be curious whether you were asking well-thought-out questions and providing reasoned answers--not what your question:answer ratio was, or what topics you needed questions and answers on. Although I see one hell of a lot of posturing, both her and on reddit, that "real" programmers would never deign use StackOverflow, most "real" programmers I know, no matter how experienced, at some point, have to use a technology they've never used before, and get stuck with something simple. The ones I'd hire at that point go ask a question; the ones I wouldn't spend the next eight hours stumbling through manpages because their pride prevents them admitting they might have a knowledge gap.