I'm not at home, and I don't want to tell you how to rebuild the bootloader without looking there first (might get it wrong). What you could do is fdisk/mbr. This will make it so only windows will boot, but you'll still be able to get into Linux with your boot disk.
Damn, I know just how to do this in Win2K, but I don't remember which files you have to edit in 9x/ME. It'll be at least an hour before I get home, and I know it's pretty late there...
You could also check on one of the Linux help sites if you'd rather not wait.