I'm a little late jumping into the conversation, but if I can throw out a few opinions (forgive me if these points have been argued already, just let me know):
1. It could be argued by purged (that's the term I've been going with) teams or cities that if they invested in stadium upgrades at the behest of their parent club or MLB's facility standards, MLB is in part responsible for that liability. It's not a hard argument to make: two parties have a contractual agreement, one party makes that agreement contingent upon an investment, and the second party makes that investment only to find the relationship terminated anyway. The attorneys would fight it out, but I imagine there are a few sympathetic judges out there that would see the purged teams' side.
2. @Centrum Hockey, I don't think that MLB's antitrust exposure is in purging 25% of MiLB teams but in their desire to control the entire baseball landscape. Consider this scenario, in which we'll focus on David Heller and Main Street Baseball, which owns one or two MiLB teams that will survive and two or three that will be purged: Lowell is on the chopping block, but let's say Heller really wants baseball to remain in the market. He has the resources, so he negotiates to buy a MiLB that survives the purge. Maybe those owners hate the new landscape of minor league ball, maybe Heller just makes an offer they can't refuse. Anyway, Heller plans to buy the team and move it to Lowell in order to resurrect the Spinners. Now MLB has already decided it didn't want Heller to own a team in Lowell, that's why the Spinners were purged, so MLB rejects the sale/move proposal. They can't argue ownership is unsatisfactory because Main Street Baseball also owns the Wilmington Blue Rocks, a surviving team in MiLB. The ballpark is good and the market is in a practical location. Any rationale MLB offers would be a transparent cover for, "We already said we didn't want him to own a team there." That's where MLB runs afoul of black-letter antitrust law without any logical or legal grounds beyond, "we said so." And while this specific scenario may not come to fruition, MLB has gone to great pains to decide which teams should exist and who they should be affiliated with. Minor league baseball's map has always been fluid; owners come and go, and markets pop up that want a team and they're willing to build a nice stadium to attract one. When MLB blocks transactions because they upset the carefully-planned pieces on their chessboard, the antitrust exemption will be at risk.
3. All that being said, it could be argued that MiLB actually benefits more from the antitrust exemption that MLB does. MiLB has carefully defined territorial rules, and leagues, teams, and prospective markets work within those rules. Without antitrust protection, there's nothing to keep a team from moving into another club's backyard. The Rays notwithstanding, MLB doesn't see much in the way of franchise relocation any more. And baseball's antitrust exemption for the most part only applies to franchise ownership and relocation; it made some antitrust concessions following the 1994 strike in the Curt Flood Act of 1998. Interestingly, the other way the minors could get hurt is that without the antitrust exemption, it has been suggested that assigning non-40-man roster players to minor league teams could be regarded as a restraint of trade, since those players are not members of a union and they have not been a party to collective bargaining to hand off those rights. Without an antitrust exemption, we might end up with a MiLB players union.
It's been said that MLB sees the other major leagues and how they do quite well without any antitrust protection, so they're not terribly worried about losing the exemption.
All of the above being said, I think it would be a fantastic comeuppance for MLB to smugly dismiss its antitrust exemption in this power grab for the minor leagues, and then see the Rays and their New York-bred owner opt to bring a third major league team to the New York City metro. The Yankees, Mets, and commissioner would freak out, then they can Google Al Davis and Pete Rozelle to see how that turned out without an antitrust exemption.
