The Community Council does take past behaviour into account when reviewing applications for prestige classes that are particularly disruptive. If there are indications that a player might not treat the RP with the appropriate gravity, or if they tend to meme around, they might find it more difficult to convince the Council to approve an application for (for example) a Shifter or Dragon Disciple, which have features that can be immersion-breaking if misused. If you're applying for a prestige class (or subrace for that matter) with significant utility in PvP or likelihood to generate conflict (Dragon Disciple, Blackguard, Shadowdancer), past behaviour in conflict might be looked at. But the Community Council's mandate is emphatically not to "punish" players. An application not being approved isn't a punishment, it's an assessment, with recommendations for what you might need to get the application approved next time around.
A prestige class is also 100% not a reward; it doesn't make one special, it's not a prize for great RP, and it isn't about being "in favour" with anyone. The application process exists to ensure that a player comprehensively understands the class they're applying for, and has met the RP requirements (How did you learn to flit between the transitive plane of shadows and the material world? Did someone teach you? How has your character learned to understand the nature of Ki? From whom? What have you done to train for being a sewer hobo? Which existing Hallowed Witch revealed unto you the secrets of the Weave?). We want to feel assured that the player will roleplay the nature and features of the class appropriately, and won't use it to go against the spirit and themes of the server.
The DM team can (and do) pull PrCs if a player is misusing them, but only as a last resort. And it isn't within the remit of the Community Council to do so. The rules are designed to afford numerous chances for a player to reflect on their actions, and withdrawing prestige classes as a punishment for some unrelated thing isn't how the Team thinks about enforcement. If you're getting reprimanded for muling items ... whether or not you're a Pale Master is beside the point. If you keep doing it, you'll end up banned, and won't be able to play that Pale Master anyway.