How were the owners able to justify and maintain a position that seemed to bring back a form of virtual economic slavery? Why and how could teams "own" players?
I think that another issue that came into play with free agency and the abolishment of the reserve clause was the additional media coverage that came with the advancement of television coverage of baseball. This allowed individual players to become more "marketable" as individuals.
The celebrity of particular players over time has led to their ability to break the "economic slavery" and negotiate for their particular talents. The ability to market individual players (not just teams) has made name brands of individual players. The more money an owner can make from a single player, the more likely he is to fight for his piece of that pie. It is one thing to sell Yankee gear, and a whole other to sell Derek Jeter gear.
I think it is important to remember the perception of players in the beginnings of most professional leagues. They weren't viewed, as they are now, as the arbiters of their fate because of their vast talents or their willingness to work super hard at mastering a very particular skill.
They were viewed as men who were playing a game and were lucky enough to get paid for it. Owners, as the previous poster pointed out, had huge amounts of power over the players and it took years and years and years for the players to fight to get the right to free agency and to benefit from their prodigious talents and sacrifices.
Prior to the abolishment of the reserve clause, players were basically bound to their team for life (or until they were cut loose or traded). Baseball owners received special consideration and were exempted from the Sherman Anti-Trust Act of 1890. St. Louis Cardinals outfielder Curt Flood first challenged the reserve clause in 1969, but the clause was not struck down until 1975 when Los Angeles Dodgers pitcher Andy Messersmith (who had played for a year without a contract) was declared a free agent. He signed a rare $1 million dollar contract with Ted Turner's Atlanta Braves. This effectively ended baseball owners' "slavery" system.