For example I could have in my setting an organization that's known for their specific abilities (a prestige class with some cool and unique class feature). Only members of this organization can become <name of the PrC>, because they don't teach it to anyone and their abilities are to unique to be self thought. So my players couldn't take the PrC and refluff it.
What if somebody kidnaps one of the members and 'convinces' him to teach it to an outsider? There are plenty of ways to do that, and if the abilities of the PrC are any good, and the organization has some history behind it, somebody would have probably done that already.
Depends on what the prestige class abilities source from, this could be a little on the thin side.
-Training/Knowledge(dervishes, etc). Much better to get an actual splinter faction from the main organization rather than to kidnap someone. You need to meet the training requirements(which outsiders probably don't know about) and then undergo extensive training. Pretty easy to get access.
-Initiation(lots of the magical PrCs). You need to perform a particular ritual or some similar rite to unlock the powers. This has obvious limitations, since each would-be member would need to meet the requirements for the ritual, know about it, and have access to the required location. If you need to be knighted at the Silver Flame, welp.
-Sponsorship. The powers are sourced from a sponsor, you're out of luck. Gods, demons lords, council of ancestor ghosts, etc, you need their ongoing support to get the abilities and they can exercise judgement.
-Talent/Bloodline. Easy to fluff, hard to 'steal'. You're born with it, or not.