i only know some of the principles of character animation, so I can't give much more than an opinion, but it sounds like what you want shouldn't be the hardest thing to do.

The top part of the model has all of it's animations made seperately from the bottom half, and the top/bottom animations get blended together by lines in the .qc file. This cuts down on the total amount of animations that need to be made. For example, walk, crouch, run, stand etc are all bottom half animations, and they all use the same shoot, stab, scratch buttocks, etc. (top half animations) There would be too many individual animations if 'walk' needed to have seperate versions for each of the top half actions. Then a whole new set for 'run' etc.

I imagine that you already know most, if not all of that.

So, what I guess I would do first, would be to decompile a player model, open the reference model in good old milkshape, and create a static pose with the legs in a sitting position. If I had a model of the vehicle that this was intended for use in, then I'd use that as a guide for the pose. When I was happy with the pose, I'd delete the vehicle, and export the .smd, and name it as one of the existing 'bottom half' animations, like walk.smd.

As long as the decompiler has created an accurate .qc file that can be compiled again, then the new 'walk' animation should have the legs in a static sitting position, but still be capable of all the original top half actions. In theory, anyway.

IF, it worked, then I'd go back and make an animated sitting pose, a 30 second loop with some twitching etc.

This would leave the problem of the player model having a broken-arsed walk, but that would be a different bridge to cross.

I looked at the sdk files last night, and tried to work out how the character animations, qc files, qci files etc, all come together to make a player model. It's too much to take in all at once, but I learned a little, and I still think my initial plan, with a few ammendments, would be the way to go.
One of the qc(qci?) files that gets included in compiling models has all of the crouch animations referenced in it. All of these animation.smd's have only one frame each, a simple crouching pose. There are no shooting or other actions in them, so they look like the perfect candidates for adaptation.

Have you tried this already? If so, what goes wrong with aiming?

I'm thinking that any problems with rotation should be taken care of by the coder.