I would check it after a couple hundred miles and see what it looks like, but it will probably be fine. usually water in the diff comes in through either the axle seals or the breather tube being submerged or missing.
What year is your XJ? the early ax-15s don't have a breather hose on them, they just vent around the shifter. the later ones have a breather tube that is built into the cap that holds the shifter in place, here is a writeup of extending the breather on the later model AX15s. http://katy.tx4wd.org/tech/trannybreather.htm