Here's an idea: Let's say you want to morph a boned mesh that's in mid-animation, into some other shape. Firstly, as Smiff says, vertex positions will appear to be at their original positions. So as you morph the vertices from those positions to the starting positions of the new shape, simultaneously 'morph' the bones from wherever they are, back to their starting positions. Once the morph is complete, it should be seamless to simply replace it with a correctly boned version of the target shape--assuming you need a different rig for it.
If, say, you wanted to morph facial expressions onto an animated character, then that's easily achieved simply be mixing boned animation and vertex manipulation.
If, say, you wanted to morph facial expressions onto an animated character, then that's easily achieved simply be mixing boned animation and vertex manipulation.