I don't see how they could differentiate the Paladin and a Crusader. Both appear to be the same save one derives it's power from their convictions while another gains it from divinity. Basically it seems like the same class with alternative fluff.
If you're talking mechanically, paladins would have a specific set of abilities that combat things like undead, evil outsiders, and evil mortals. They would also offer very general benefits to their allies, like courage aura and healing powers. A framework might work something like this;
Lay on Hands
Crusaders would get abilities that tie-in specifically with their gods. For example, a crusader of Surtur might be able to wreathe his weapon in flames, place fire resistance on people, and provide attack bonus aura against things like elves and dwarves.
Paladins should be general good-guy lightbringer types, like Roland, Luke Skywalker, and Cecil Harvey. They are champions of Light and Life, and their abilities reflect that. I do think deities should have their champions, and I think that appropriating the paladin to fill that role takes away from the heart of who and what the paladin is. I also think that the idea of a crusader is big enough to warrant its own class, and that crusader abilities should reflect the god they serve.
I think I'm going to make a Crusader of Boccob that gets a spell-channeling attack, the ability to grant others and himself spell resistance (Lay on Handsish ability) and an aura that grants all within it save for himself a +1 caster level. Well, that wouldn't be making a new class so much as it would be coming up with abilities for deities, making the crusader's abilities deity-dependent, as it should be. Hehe, that would be awesome. I could get behind a crusader like that. Hell, it doesn't even have to truly be it's own class, you can just use the "crusader variant" option that replaces the paladin class abilities with unique deity-specific abilities of semi-similar nature. Then the paladin variant can be its own thing.