First, fix the MBR so it has standard boot code instead of GRUB. This should remove the Partition HD (Linux) option.

Then use a Linux Live CD to reinstall GRUB to a partition instead of the MBR. It can be the Linux partition or a new Linux Boot Partition. Only the partition that contains GRUB needs to be listed in the MBR for Linux to boot properly.

Edit the GRUB menu so that it doesn't include Windows or Mac OS X since you'll use rEFIt to boot those.

Use gdisk (gpt fdisk), fdisk, or iPartition to edit the MBR so it includes only the partitions that you want in there. Only partitions that require BIOS to boot (Linux, Windows) need to be in the MBR. For a partition to be visible to Windows, it needs to be in the MBR (e.g. if you want to see the Mac OS partition in Windows, it needs to be included in the MBR).