I'd say you have done it about as easily and safely as possible. I know that the decks were "designed" to be driven over, but I can assure you that it puts a LOT of stress on the deck guides and sheeting, and I would never advise anyone actually doing it. I have done it, and it doesn't seem to hurt anything, but it cannot possibly be good for the deck. Typically, if you jack up the front end, you can slide the deck out without removing the wheel, but removing the wheel may be easier and safer, keeping the tractor lower to the ground. Regardless, I'd say that would be the way I would do it too.
1951 Farmall Cub, Cub Cadets 102, 104, 1811, 1864, Simplicity Legacy XL 4x4 Diesel with FEL, 60" mower, 50" Tiller