I think you're mixing up things, you cant delete windows bootloader, windows obviously wont boot without it, you are confusing the bootloader (the one who kickstarts the os) with the bootmanager (the one who lets you choose which os to boot) that is active and shows the boot menu.
The boot partition determines which bootmanager is active, but when you choose to boot windows in chameleon, you would still see windows bootmanager.
In latest versions of chameleon you can set the partition to boot by default using the "Default Partition" argument in the boot.plist, you would have to change that to your windows partition

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AsRock P45TS | C2D E8200 | GeForce 8600GTS
Mac OS X Snow Leopard 10.6.1 + Windows 7 Ultimate 6.1.7600 + Fedora 11