I voted for removing the small weapons altogether. Ideally, you'd just move them to the back, but I think body variety is cooler, especially with mutations. I'd even be fine with removing all weapons if necessary, but I think removing the small weapons is a good compromise.
Another option might be to only show certain weapons with certain body types? Like, if all the "normal" human sprites can easily display some weapons, but adapting them to all the possible mutations is a problem, then just show them for the first set of sprites, and remove them from the troublesome sprites.