I'm not positive whet your problem is exactly, but I tried this:
Create a folder in my Temp directory called "DELME"
Create a zip file in my Temp directly called "DELME.ZIP"
The following code worked:
Directory.Delete(@"D:\Temp\DELME", true);
The folder was deleted.
Recreated the folder.
Directory.Delete(@"D:\Temp\DELME.zip", true);
The command threw an exception, as DELME.zip is not a folder.
Checked both present.
File.Delete(@"D:\Temp\DELME");
Threw an exception - unauthorised access (it is a folder, so yes it would fail).
File.Delete(@"D:\Temp\DELME.zip");
The zip file was deleted.
All of that looks fine to me: what are you doing that could be different?