the fact that it behaves the way you describe it with any theme change is good clue that what you search simple doesn't exist. at least nobody seems to bother if so.

not only qtapps stay alive but with every theme change a part of the old theme stays. guess that rules out a qt problem. as it seems to be generic.
well if you find something you might want to tell the themes maintainers about it. would be a great improvement to change themes without rebooting.

otherwise the issue looks quite familiar to me.
what i have to offer you concerning this is:
a) processgroups
b) lsof, fuser and the like

yes, busybox is crappy. you will want some working tools if you are looking into this...
as a sidenote you might get into real fun if you look closer at it.