Re: 55 Johnson CD12 Lower unit
Maybe someone has a better trick, but I do it with a combination of yanking with a vice grips, cutting with a dykes, twisting with a needlenose pliers, etc. Rip the $#@! out of the old seal; just don't use the aluminum seat or any part of the aluminum lower unit housing as a fulcrum for prying. If you need to pry, use a piece of wood under the pry bar for a fulcrum. Your instincts are correct.
I've seen the coolest slide puller tools for sale that screw into the handle of a vice grips. I want one! That'd work great for stuff like this.