This is how I would play the situation if I was the DM:
I would rule that a paladin who in inflicted with Lycanthropy at low level whom then gains the immunity to disease should still have to live with the effects of the curse. That is every month he will involuntary shift on the full moon. I would argue that he is immune to any new disease but, suffers the old ones.
If he learns that he is an afflicted lycanthropy of a type that is inconsistent with his god (ie. any lycanthrope that does not have a Lawful Good alignment) and does not try to contain it will loose their paladinhood. If they try something and it fails once and they try a second time without changing/improving the method, looses their paladinhood.
I would allow them to learn the Control Form skill, found in MM, but can only use it to prevent the transformation, if they can find a acceptable teacher, like a cleric or paladin afflicted lycanthrope or a Natural lycanthrope with a Lawful Good alignment. This would only be a short term crunch for them not a permanent fix.
If an accident occurs and they get loose and harm/injure someone, the paladin needs to make some sort of amends to the family of the victim, to atone for the beast. If they refuse to try to do this they imperial their paladinhood (lose some class ablilities).