Clarett's talent is irrelevant. Mike Williams was a sure-fire top-5 pick and, although he wasn't filing the suit, the decision would have made him draft eligible.
Your point about the strength of the NFLPA relative to the league is valid, but I see this as a sticking point for MLB. I can see a long, drawn out, protracted legal battle over this issue, because, at heart, what would be up for decision, is the right of MLB to determine playing eligibility. And, we aren't talking about MLBPA members. The guys coming over from Japan are potential members, but they don't belong to the union until they sign a contract. How hard would the fight from MLBPA be for potential members? How hard would it be for people who will likely unseat current members? Tough to say.