Hmmm... first, that's a bad definition of minor leaguer. Lots of minor leaguers get called up in September to get a taste of The Show. The definion we're using is that a minor leaguer is someone who hasn't accumulated a year of MLB service time (in other words, would qualify for the rookie awards if they played in the majors that season) and isn't starting the current season on a 25-man roster. As far as what to do with them after the season... returning them to the player pool is silly and makes them completely pointless. You'll let people draft players to the future but not let them keep them once they get there? That's just being lazy and not wanting to research the minors.
We do a keeper auction league and here's how we do it...
All players can keep 4 normal roster players whose salaries go up $3 the first year, $5 the second year, and $10 every year thereafter. In addition, they can have up to 3 minor-league players whose salaries up $1/year. So basically, minor-leaguers should be free to keep or at least cheap because that's the only reason to have them. Otherwise you may as well draft NFL players onto your rosters since they'd serve about the same purpose.
0-3 to 4-3. Worst choke in the history of baseball. Enough said.