When I started with emacs, there were some bindings that would make my hands ache after a day of use, usually from the transition between difficult keybindings, not any one key combination in isolation. One of the first things I did was add in the ergoemacs bindings, and I never regretted it. It's not as if doing so made me suddenly forget what the old bindings were, although I am slower during the rare cases when I'm on the normal keybindings. But it's a small price to pay for not having my fingers hate me.
Editors are meant to be customized to your workflow and what works best for you.