If you can fire pellets out of the well using a mass driver, I'd think that firing whole spacecraft out is going to be a much more viable option than trying to reduce the depth of the well to any noticeable degree.

Yes, spacecraft are more fragile than pellets, and canned primates even more so, but a ludicrously long acceleration track is still going to cost peanuts compared to the kind of planetary liposuction you're talking about.