The problem isn't with Paladins and Rogues, it's with Paladins and Thieves. One group I play in has a Paladin and a Rogue, who probably couldn't pick a pocket if she tried. She's great at sneaking, picking locks, and archery (Arcane Archer PrC), and is Neutral Good, the real adventurer's rogue. Not a thief at all.
The problem is with conflicting character aims, and the Paladin mindset isn't compatable with a lawbreaker/borderline evil type at all. When making a character, I make sure that there won't be too much party conflict. Some can be fun (competing priests for instance), but mutually exclusive ideologies will probably be too disruptive. You were probably better to go rogue as well. Rogues in numbers can be pretty frightening, after all.
--Seule