Although i never tried this program personally, i was referred here by a friend. The program can disable a selection of keys, i think including that windows key. It is an XP/2000 only program, so I ended up modifying the registry, which leaves the key disabled/enabled unless i edit that and restart.
While it is possible to disable the windows key by modifying the registry, doing this leaves the key disabled all the time and requires a restart if you wish to change the behavior.
A better solution (if you are using Windows 2000 Service Pack 3 or Windows XP) is to use the Windows Application Compatibility Toolkit, which you can download from Microsoft. This allows you to disable the windows key for specific applications (in this case Diablo II), while allowing the key to remain enabled for everything else.
To set this up after downloading the toolkit from Microsoft, follow the instructions on this page. The instructions provided are for playing FFXI, but you can simply substitute Game.exe (from your Diablo II directory) instead of Pol.exe and it'll work fine.