I'm not familiar with MLB Real GM League, so I don't know if this will work for you, but CBS SportsLine allows 30 teams in upto 4 divisions. It is decidely not free, but with 30 teams it would be less than $5 per team. Just the commish pays, then you enter your owners and the site sends them invitations with all the information they need to get started. We've used it for about 6 years and like it.
http://baseball.sportsline.com/splash/b ... /spln/mgmt
edit: I forgot to add that you can start a league for free and look at all the options, rules and such. I think you have 2 weeks to pay for it, but I'm not sure if that's two weeks from when you signup or 2 weeks into the season (I think it's into the season).