I think you are missing my point. The Nukes were built by the soviets, but after the breakup, Russia had control of them in Ukraine. In order for Ukraine to take full possession of the nukes in their country, they would have to fight through Russians at military bases.
My point is basically that if Ukraine tried to take full control of the Nukes in their country, they would have been picking a fight with Russia, and possibly the US as well.