You can format the partition with Linux on just fine, the boot loader will be arsed (Mosy likely GRUB) but that is fine as Windows has its own Boot Loader which GRUB overides i believe... not qwite sure how the boot loader works but i know u can format a linux partition and windows will still work :) also i suggest if u want ur partitions back to windows then download the gParted live CD and boot up from that and use that to format the partition with linux on it then resize ur windows partition to take up the rest of the drive.
Another solution would be to download and burn PCLinuxOS MiniMe, boot it, and use "DiskDrake" to remove the partitions. There are other live discs that have partitioners. eLive is good too, it has GParted. Knoppix is the best for older computers, and it has QTParted on it (Last time I checked...).