You can switch out the calipers if you wish. The nanny and the ABS controls won't care, as long as you don't mess with the ABS sensors. Those are separate from the calipers and not a part of it. As stated above you 'could' run into some feel and control issues related to the master cylinder and the fluid flow rates. The biggest problem you'd have is the dimentionality of the calipers. Set back, bolt patterns, etc. All of those problems could be overcome if you want, but it could be a lot of work and a lot of trial and error.
Older V-Strom owners switched front brake calipers for years to improve braking and feel, since the original calipers were garbage. (I was one of them.)
Braking is science, but not rocket science going to Mars and back.