The Eraser download page states that version 5.7 (which can be downloaded from SourceForge) is the most recent version that can be used with Windows 2000. Do remove as many traces of Eraser 6 (including Registry entries) as you can find before installing 5.7. Hopefully, the install crashed before it copied anything to your system.
If all you are trying to do is wipe an old Windows 2000 system, you might wish to look at Darik's Boot and Nuke (DBAN) - details in the companion forum to this one.
6.0 was not designed to be interoperable with Windows 2000, for the simple reason I don't have that OS and I can't exactly procure it legally now. In any case, it is near the end of its product lifespan (it is in the extended support phase from Microsoft) so I don't really see any reason that we should support it. So yes, the workaround is to use v5.7