Hrmm, I in the battle of evil vs. good, is it not the idea that evil will do whatever it needs to, to accomplish it's ends. Good will do what it takes, as long as it is moraly free of causing others to suffer, that is their end. What I think might be cool, is if goods could instead of simply killing, allow them to capture their prey. From their RP would ensue, and the victim of said capture would basically be tied up or something of the like, and "incarcerated" for a period of time.
I think that instead of trying to justify a reason for a good aligned player to use maledictions, perhaps there should be a class that can add effects that weaken resistances. In some forms, they do exist in the already offered classes, however, what I would like to see is clerics get more options like the ranger, warrior, etc. as far as skills/spells. I think this offers a lot more unique opportunities for specialization, and perhaps more RP ideas. Instead of simply receiving a bonus to bless combat wise, a cleric of combat would also receive larger ac bonuses, more combat related spells, such as (dare I say it) firestorm(that might be a bit too much, but something to consider). They would not have the same healing ability as a lot of the other clerics, but this is to balance things out. Perhaps even limit combat clerics to spells that do mostly physical damage, whereas the others would generally do magic damage dependent on their respective faith. I realize that this would make shaman's and healer's have to be absorbed into clerics, but we could limit things down into more core classes, and you get to choose path's and possibly even multiple skill/spell groups within various classes.
I realize many might argue that this would greatly change the game. I would assuredly agree, but the game is going to continue to grow and change, and I think a more skill based game would be an excellent way for us to head towards.