Here's what I don't get about your argument.
Even if an employee thinks that a video is copyrighted, does the employee have a responsibility to determine whether the person who posted the video actually held the copyright? Because, you know, if the copyright owner opted to upload it to YouTube, YouTube would be violating no laws.
So if an employee suspects that content is copyrighted (because, unless they posted it themselves, they couldn't really know), in order to discover that it was illegal they would then need to ask the poster about the copyright ownership. Does the employee have the responsibility to do this? Does the employee even have an ethical obligation to do so?
So now if we're talking about copyright violations occurring on YouTube on a massive scale, but still only a small fraction of the total uploaded content, does YouTube have a legal or ethical obligation to confirm content ownership? The answer to this, under the DMCA safe harbor clause, is "No." YouTube is, however, obligated to take action if someone claiming to actually be the content owner says, "Hey! I didn't grant rights to upload that!"
It'd be a lot harder for YouTube to maintain safe harbor protection if its employees perpetuated the uploading of copyrighted content or ignored take-down notices. In this case, even though it appears that a founder may have uploaded copyrighted content, the other founders got him to stop. Because of this, I personally believe that the founder (Jawed) could find himself outside of the safe harbor protection, but only liable for the content that he uploaded. The company might even be found liable for this amount as an extension of that owner. Still, the damage plus penalties for that small amount of content are significantly smaller than Viacom is asking for. (If Google were found guilty and liable for $250,000 in damages, would Viacom declare this as a victory?)