Use the 7-Zip File Manager to delete them.
If you are still having trouble, ensure that you utilize Shift+Delete inside the 7-Zip File Manager. Otherwise, Windows tries to move them to the Recycle Bin (which will fail again).
There is a flaw in your line of thinking.
Thus, to my understanding, writes to Program Files should primarily
only occur when installing an application. This makes compressing it
not only a huge source of space gain, but also a potential candidate
for performance gain.
Virtual Store is not used if the program is running as Admin. In the case of Setup Programs, this is all setup programs.
It's very rare to run into a program that isn't UAC aware these days and where VirtualStore takes over. For example, my Virtual Store only lists Foxit Reader.
Compressing it though, does look interesting. In my case, compressed my Program Files out of curiosity. My most disk intensive programs is the Total War series: Napoleon, Empire, Shogun 2. In particular, switching between Battle map and the Campaign map involves a heavy amount of reads.
I decided to compress the Steam folder and fire it up a few times. Predictable, since the game loads require heavy sequential reads, it was slower. My map loading times went from 38 seconds to about 48, although it actually took over two minutes my first time loading.
I haven't tried other applications.
Best Answer
Assuming NTFS here, in which case the technical limit is around 4 billion files. And until you go over 10s of thousands per directory you really should not worry too much.
Note however that programs like Explorer suffer much sooner than 10s of thousands, because they try to access all files in a given directory to get meta-data, etc.