In the latest Trunk, there's only 6 obsolete classes, as the recent Environment changes fixed the two of them. The following script, adapted from your post above, cleans them up nicely:
Running "Smalltalk shrink" then complains about two obsolete behaviours, and I this is a bug with Installer. If I just close the debugger and inspector, collect garbage and then run "SystemNavigation default obsoleteBehaviors" I get an empty array.
So it looks like the shrink works. It doesn't do much, though. My image goes from 20.9MB, down to 20.3MB.