Setting case to invert by default fixes a lot of those problems (you just invert the case again before passing the string onto the shell).
Also, for doing many shell things fork/execv is the only thing that gives you sufficient control, so I suggest avoiding run-program and using those instead.
Oddly enough, just last week I was trying to do some scsh-like things with Common Lisp, and I ended up banging my ahead against its case-mapping behaviour (Common Lisp upcases input by default).
There’s definitely an opening for a Lisp version of something like scsh. There’s some tricky stuff to be aware of (e.g. SBCL’s RUN-PROGRAM puts processes in a different process group, which mean C-c does the wrong thing), but done well it could really be awesome.