Remember that the Gefs, at this point, have GTVA support. Stealing the ship within 10 minutes isn't impossible, not for the GTVA. Especially, not for the GTVI (who I believe would handle the operation).
Now, if you're talking about before the war, then that's different.
Still, it doesn't match with the mindset of the military to destroy a ship like that, it doesn't match with the politics of the ruling party either. Taking apart the ship's materials wouldn't help much because of the obsolete parts, and it might cost more to do than just use materials they have on hand.
It makes much more sense to just throw the ship somewhere out of the way, and forget about it. (a museum to remember the mistakes of the past, perhaps?) (er, yeah, I see the irony in what I just said, but it still applies.)
Also, Pluto, as a place to toss old stuff, comes to mind again. It would also be a good reason why no one could use the hulk anyway... too far, too risky to go get it.