I think the NCAA's likely to come to the same conclusion with or without Pete Thamel casting light on what has been alleged.
It's not an organization that traditionally cares what people think of it.
As for the source "claiming to be misquoted" I'm going to guess that happens to every reporter on almost every story. I forgot where I read it, but someone said that a journalists greatest skill is getting a source to disclose information that would probably be harmful if it came out.
Now I don't know if the Asst. Coach realized it as soon as he said it, and asked for Thamel to not use it(he'd be under no obligation to honor that request) or if he said it, thought it would be okay and then saw how it looked in print and said he was misquoted or if he was in fact misquoted. But the fact that Thamell's been accused of misquoting a source on two stories, is no stranger than two seperate UK recruits being accused of improperly receiving benefits. In fact it's probably much less strange.