Clint had Meredith in tow during the most crucial time (the moment Brian disappeared), and for her to be willing to take a polygraph even though she had an attorney by then (when they almost always advise against it)... that's really compelling. She had to have known nothing. It's almost like if Clint did know anything, it couldn't be about any incident (eg. assault gone too far/accident) that happened at that time. It could really only be about Brian having intentions to disappear... if anything.
Maybe an investigator just interrogated Clint too aggressively in the first instance, and his actions afterwards were all about that. It can suck being one of the last people to see someone alive, that's for sure.
I’ve always been of the belief Clint and Brian probably did drugs that night and Clint didn’t want to incriminate himself. Could have been something relatively harmless like weed (it was 2006) or even a party drug such as coke or ecstasy. I don’t see how he could know that much because there wasn’t any feasible opportunity for him to do anything to Brian.