A less messy variant of that idea is to use just one global array called @garbage, and push references to your large hashes onto it.
That way you would at least only have one global to worry about, and your structures would still stick around until the end.

The response to the post you linked to sounds like it should solve your problem, provided that you have the ability to recompile Perl on the target systems: Re^3: Sort taking a long time to clean up