Get "TweakUI" for Windows ME/98. It's downloadable for free from Microsoft.
When you have it installed, open your control panel and double click on the "TweakUI" icon in there and go to the "My Computer" tab.
You will be able to un-check your "D" drive letter from in there. That way it won't even appear in Explorer as a part of your computer as far as Windows is concerned.
I did exactly the same thing on my Windows 2000 installation on the machine I dual-boot Slackware on.
EDIT
Here's a link to TweakUI on Microsoft's site for ya.