in the heat of the moment you can’t shoot a scumbag?
It'll be up to a jury to decide, but if it went down as described, no. It wasn't a legal shoot, at least in my state it wasn't. You can't shoot someone when they're running away. That's the law.
“I come back and they see me with a gun, and they run,”
If this means he was out of danger, then retrieved a weapon and gave pursuit, that would be hard to characterize as heat of the moment.
I’m no lawyer, but ISTM this will come down to admissibility of evidence. The surviving burglar probably will not appear to testify, so it will be about ballistics and whatever statement he may have given to police. Also about police procedure: was he Mirandized?