I am picking this up in the middle, but could you
use inositol selection? If you have ino-, leu- it should
remain viable in -Leu medium, but the LEU+ will die. Inositol
selection should be pretty general as a means of selecting against
prototrophs of various sorts. One problem is that you might not have the
ino- marker in your strain. I would guess that the easiest way to generate
that would be by targeted disruption of your starting strain.
A selection similar to this was described based on thermotolerance,
but this was not very effective in our hands.