Yeah, I think that "high prices for low cha characters" equals "high prices for shy characters". Like the real life: I'm a shy girl, so I can't haggle, so I usually buy stuff at stock price. A charismatic person would've gotten a discount.
Technically, usually the question is solved by introducing an optional component, or several, so the player chooses which setup to get(reputation only, charisma only, high cha discounts but no low cha punishment, high cha discounts AND low cha punishment and so on). Best of luck with this stuff. If you're not very familiar with coding, by the way, check the tutorial section over there. Echon posted the links just recently in another topic:
http://forums.pocketplane.net/index.php/topic,28155.msg329765.html#msg329765