You can get Zeus to recover deleted groups by running code like the following:
{deleteGroup _X} foreach allGroups;
That is:
1) Follow directions to reach limit.
2) Delete some groups (note even after deleting groups you cannot place any more units)
3) Run above code
4) Notice you can now create groups back up to the limit.
This causes issues on dedicated servers that run for long periods, since Zeus may be used to run multiple missions without a restart.
Currently my group is working around the issue by having the above code run periodically to 'free' unused or deleted groups so Zeus can continue to work.