Some random half-baked ideas:

Assuming for the moment we want a general solution to allow
setting uname info on a per-process basis.  (User a is running
a browser while user b is running matlab.)

What if the utsname structure became a per-process structure,
inherited across fork?  Then we add setuname() to change the
various fields to whatever we want.

Then we write a small wrapper program to set the desired uname info
and run the real app.

If the app only uses uname(1), life is easier:  have the fake uname
echo $UNAME, and have the wrapper set $UNAME.

For getting #! to run the correct program, chroot might be
helpful as a workaround until the kernel does the right thing.

-Dave