Well, holy warriors of differing alignments is pretty common. Most I've seen kept consequences for actions not in accord with the class' alignment...though which actions qualified differed, of course.
A non-alignment based command over beings like angels or devils- instead based on their extraplanar nature is certainly feasible, but absent a bit mire detail, it leaves unanswered why a good cleric should have power over the extraplanar servants of good (assuming that power includes being able to banish them against their will).
As I've said a few times in those Paladin threads, for godly types slaughtering the innocent, I always chalk things like that to what I call the "Old Testament/New Testament" dichotomy: in the OT, there is a lot of slaughter; in the NT, it's virtually absent. (Relax, this is about themes, not theology.)
Part of the reason is that one of the virtues most highly held is mercy, whereas the OT narrative contains a lot of judgement and revenge. In the latter, humans are sometimes directed to slaughter every man, woman, and child by God; this is thus a positive because the victims were judged to be irredeemably evil. In the former, the main slaughter of innocents is seen as an evil because it's targeting the hero of the narrative, who extolls mercy, love of enemies and peace.
And both types of themes, each ethos they describe, can be found in tales of holy warriors from myth, legend and fables of antiquity to modern fantasy novels.
In that situation, it's less about the god or the PC's alignment, and more about the interrelationship between worshipper and worshipped; about sects. If you look at RW religions one sect may see only the dark side of their faith, others only the light, and others see the gray, each with variations in what they believe their faiths condone or condemn.