Oh, tsuwm, I was afraid someone would bring that up, and it would have to be you! Here's what Atomica has, under discomfited:
USAGE NOTE It is true that discomfit originally meant “to defeat, frustrate” and that its newer use meaning “to embarrass, disconcert” probably arose in part through confusion with discomfort. But the newer sense is now the most common use of the verb in all varieties of writing and should be considered entirely standard.

No, it doesn't say which of the two is more common, but I thought the history was interesting.