The main reason not to morph the eyes (too drastically) is that you don't want them to move the geometry off (the rotation) centre.

If you find morphing the best solution to repositioning the eyes, use it, but expect problems if you try to rotate them.
Most, if not all, of the "difficulties" you mention are solvable once you know enough about the CR2 file structure.

When exporting OBJ files from Blender to Poser, you'll need to change the grouping options to write group information as "g" lines, and you'll need to fixup the naming.
If Blender is still reordering the vertices, that can be fixed, but we'll deal with that if you run into that problem.