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The joke that Obama was trying to make was not that his poor bowling score is comparable to what Special Olympics participants would score. In fact, I'm sure that if bowling is a Special Olympics sport (and I'm not sure it is), they'd be kicking Obama's and most other people's asses.
The correct context was that Leno was complimenting Obama on his bowling, Obama knew that his score was not worthy of praise, and Obama commented that Leno is complimenting him like people compliment people who participate in the Special Olympics, i.e. no matter what he does people say "Good Job!" and the like.
I don't know if this is any less offensive -- I think it is -- but it's clear in this context that he wasn't directly insulting the Special Olympics.