While we don't go out of our way to make these differences, we are fine with them happening from time to time. In the above example with Nefarian's axe, we chose to go that route because historically, Nefarian also dropped a similar type axe in Blackwing Lair. We also like the idea of weapons being on an "end boss", as they generally are quite sought after items.
That said, Firelands will be dropping two weapons suitable for Enhancement Shaman that do not involve killing Ragnaros. One of these will even be able to drop from multiple bosses.