Depends, really, on the DM's take on the 'sanctity of the dead.'
By default, the dead aren't really special in D&D. The corpse of your ally or your enemy is the same thing -- a corpse. It can be used to raise them later (but might not be needed), or to make an undead out of it. There's no real concept of preservation, because a corpse is only as useful as what you can get out of it. So looting a corpse isn't bad. Desecrating one is mean, but depending on what the cureature was in life, it might not be evil (skull-banging a beloved king is probably CE; chopping up the body of the villain may not be exactly honorable (e.g.: the paladin would have problems), but it's certainly not wicked). Turning it into an undead is only evil because the spell, by definition, creates more evil in the world.
So by looting the corpse, the rogue wasn't nessecarily evil, and the paladin might've had a few issues with it, especially if he was chopping them up or something. But neither were you wrong in defying him -- your character could want to hold himself to higher standards than the rogue's.