The reason no one whined about towing the ship the first time, was because nothing drastic or expensive had been done to the hull yet. If it sunk along the way, too bad.
But after it's spent time (and lots of money) in the yards, the "vested interest" becomes much greater. I doubt the ship itself is any less seaworthy, just people are less inclined to risk it.
It's also being argued that this is an atypical situation, due to the Oriskany's size. This is the biggest ship in MARAD's inventory to junk. The other ship's are not anticipated to have nearly so much towing concern, as they are considered less valuable and more easily "towable".
Funny thing is, before I heard about this a couple weeks back, I had read how some admiral in Pensacola was moving political heaven and earth to make sure the Oriskany went THERE. This ship is one big teeter totter between the eastern and western Gulf of Mexico. It'd be ironic if the Oriskany ended up going to the Atlantic where those other states submitted a joint bid. Forget which states (Georgia and South Carolina I think).