hmmmm....not plan for them? Then how will they get to the point they need? Many of the Prestige classes have unusal skills needed or built up. In directly, players will never use them still.
They can still qualify for them, but chances are that they'll do it later. I like that, because while I find most prestige classes unbalanced they wouldn't necessarily be so a few levels later.
Or, I'll do what I often do, which is change the requirements if the character is appropriate.
Only the roleplaying requirements really matter to me.
There is one exception to this: if I make it clear that certain organizations exist, the players may certainly write it into their origin that they have every intention of "trying out" for the prestige class.
On the free will issue, why is not letting people use PrC's a limitation on free will?
If a student can't make it into Harvard because he doesn't have the grades, that's not a limitation on his free will. When PrC's are organizations, that's a possibility.
Furthermore, what if a player wanted to play a Jedi in a D&D campaign or a ninja in a Call of Cthulhu game? It just doesn't fit the genre.
If "free will" means "letting my players do whatever they want even when it doesn't make sense" then, yes, I will limit free will.