I think there are a number of reasons for the Free Agent Drop Penalty. In the major's you can't simply drop someone from your club if he is hurt, you must put them on the DL. So the DL doesn't give $ back to purchase on another player. In MLB, Teams have a large amount of players connected to the Team including the 40 man Roster and all the minor Leagues. It would be too much work for a strat team to draft all the available players MLB has under contract to bring up someone new.
So If you release a MLB player you have to continue to pay his contract
and usually an additional penalty
in order to get out of the contract - it is very costly for the Team to let someone go and they don't usually get ANY $ back, in strat we Do get $ back...
Also in Strat there are so many Quality players available who are not under contract - Not so in MLB. Additionally in Strat we would simply purchase all the best high injury players who have lower salaries, then swap them out with no penalty when they get injured - not so in the Real MLB.
It would throw off the competitive balance in Strat...
I hope this makes sense.