Its my understanding that the CVN-65 will be torn apart to safely dispose of the nuclear reactor.
From wiki:
Newport News Shipbuilding will deactivate and de-fuel the ship, which will then be formally decommissioned once all nuclear fuel has been removed.[68] The process is scheduled to begin in mid-2013 and be completed in 2015.[14] Once the Navy dismantles and recycles the ship's reactors, there will be very little left to turn into a museum;[64] virtually everything two decks below the hangar bay would have to be cut apart.[64] What remains of Enterprise following 2015 is currently scheduled to be taken to Washington state for scrapping.
A good reason that the Enterprise wouldn't make a good candidate for a museum.
The first nuclear designs weren't all that good, and took up a lot of room in the lower decks. There were 4 of them on the Big "E", and they were pretty big, with plumbing snaking throughout the lower decks. The newer ones were much smaller and compact, and only 2 of them, one on each side contained in a single compartment. to remove them, you just cut out that section, remove the reactor and all the associated equipment in one shot and plate over the hole.
Similar to how Subs are decommissioned.