I think one of the nastiest consequences to deal with from having an evil party in SoD is the exorbitant prices in the store within your own camp! Check out how much I'm expected to pay for 80 arrows of ice! *shivers*. (That's 375g per twang!)
I'm sure characters with heroic reputations wouldn't experience this.
That's almost my entire current holdings. It's ironic that they effectively punish you for getting ahead against the crusade, but that's what you get for trying to make evil pay, as they say.
It's great fun finding ways to survive and get around this. Also, I like that companions are true to their alignments and leave if your reputation isn't to their liking; I wanted to see more of this in Pillars of Eternity. What I don't particularly like, is the game not having the balanced amount of companions for the player to adequately deal with this situation. It's pretty clear that overall, the game does much better at catering to the canonical traditional player. (Jaheira, Khalid, Minsc, Imoen, Dynaheir…)
For those that have finished the game, I'm currently up to the Boareskyr Bridge map. Having completed every map before this, how far through would you say I've come? Just curious.
Whilst it is a shameless plug, here's some journal entries I wrote from my last time through BG: EE. Hopefully Watchers will get a laugh if they haven't already seen it.
http://www.rpgwatch.com/forums/showthread.php?t=21933
Edit:
I tried donating some gold to Mizhena and others to influence the merchants, but the the effect wasn't too noticeable and ultimately doesn't feel worth it both practically and role-playing wise.