Considering the interaction, I see a number of possibilities:
Your friend is just going for the cheap, obvious joke, and means nothing by it.
"I am a skeptic.
"Oh, I doubt that."
There is no need to respond.
I tend to use phrases like "I try to be a skeptic" or "I like to think I am a skeptic" just to avoid that comment.
Your friend is a skeptic, and is just expressing an initial, weakly-held, default stance before going and looking for the evidence to refute it.
There is no reason to respond (except perhaps to check back later to find out what he learnt.)
Your friend isn't a skeptic. He is just a person who likes to be contradictory, and thinks calling that stance "skepticism" makes it okay. Did he check out the site at all, or look for any evidence to refute his position? If not, he is not acting skeptically.
There is no reason to respond
But suppose we were to respond anyway.
Is this site "healthy"? That term is too vague to respond to. What does it mean to be healthy? For whom?
Is this site a good source for learning the truth about dubious claims? That is a bit better. It is certainly a claim that one can be skeptical about.
I am old enough to remember when Wikipedia arrived. I gave it very little chance of succeeding. By rights, it should have degenerated into the sort of mess they have on Yahoo Answers. There was no way crowd-sourcing facts should work in theory. But, I was convinced by the evidence. It is now an amazing resource. You should NOT trust it on controversial subjects. You should double-check all of the important claims. But as a quick source of definitions and backgrounding on a subject, it is incredible.
I offer the backlog of Questions and Answers as evidence that Skeptics.SE is similarly an awesome resource. Pick some questions at random. Pick some questions on topics that you know well. Examine the answers. Check the sources. Do some equivalent research to see what answer you would have given. See for yourself whether this site does what it says on the tin.
I can intellectually point to conceptual flaws in the way we let any old person vote on answers. I can intellectually point to the backwards burden of proof. I can intellectually come up with plenty of reasons why Skeptics.SE should not work in theory.
But, I am a skeptic, which means the empirical evidence outweighs the theory, and I think the empirical evidence clearly shows the users have produced an wonderful resource to help stem the tide of lies in the world.