Agree with everything you wrote except the above. Basically the disagreement is on the source materials - one is a naive Viacom and the other is an indictment. So I think the indictment is cherrypicked "better" than Viacom managed.
If e.g. the FBI/DOJ were going after youtube I think they would have quoted more selectively than Viacom did.
Unless the full text of Mega's emails are out there - I can't be sure there's no conflict, I'm sure someone could dredge up him ordering something taken down.
Again with "repeatedly" and "specific" - the youtube emails, for all their conflict are repeated and specific, many times. There's also instances of youtube employee's grabbing stuff from other sites and putting it there themselves, which mega are accused of. I'm pretty sure with youtube's channel system, copyrighted content is paid to be put there in the same manner, though I'm not sure how youtube's early users were compensated.
I doubt the thought occured to them to bring a criminal case against youtube - that's one of the points I'm wildly speculating on - or if it was the case, lobbying stemmed it.
I'll have a read of the ruling: (PDF) http://www.legalbytes.com/uploads/file/Viacom-YouTube%20%28G...