Dan,

> Here's the stack that ends up doing full garbage collects 
> which, it can be argued, is not incredibly smart here.

Well, I'd say it's pretty smart since it's only a fallback position. 
Two ways of fixing it:
#1 Make #isZipArchive open the file in *read only* mode. Failure to open
an existing file is almost always due to some sharing violation which
usually means that you're trying to open a file in write mode that has
been opened in write mode already. So just change #isZipArchive to use a
read only file (it doesn't need to write it so why even try?) and that
possible problem will go away.
#2 Find the place that opens the file and doesn't close it. Since the GC
is only triggered if there is an open file by that name in Squeak
somebody *must* have a handle to it.

Cheers,
  - Andreas