Are you seeing multiple Linux icons in rEFIt? If not, I'd just leave it alone, since the extra boot code is doing no harm. If you are seeing extra Linux icons, though, you should first check that none of them refers to an EFI boot loader that you're not using. (Check the description that rEFIt shows when you highlight an entry; EFI boot loaders normally show a path to the boot loader, like
EFI/ubuntu/grubx64.efi.) A stray EFI boot loader would be the easiest to remove, since it's just a file on the disk (probably on
/dev/sda1, your ESP).
If you're sure you've got extra BIOS/legacy boot loaders showing in rEFIt, you can remove the unnecessary code by using
dd, as in:
sudo dd if=/dev/zero of=/dev/sda2 bs=512 count=1
The details vary depending on what you want to wipe, though. Applied to the MBR (
/dev/sda), you'd set
bs=440 rather than
bs=512, so as to erase just 440 bytes rather than 512 bytes.
This procedure is VERY DANGEROUS. A mistake can make a partition, or even your whole hard disk, inaccessible. Thus, you should be very sure that you're wiping out the correct data. You haven't presented sufficient evidence for me to be confident enough to recommend wiping any specific location. If you want more advice, post a link to the
RESULTS.txt file produced by running Boot Info Script. That will produce detailed partitioning information and data on what boot loader(s) you have installed.
One more comment: If you determined that your Mac needs to boot in BIOS mode to get an X display prior to installing Ubuntu 12.04, you may want to re-examine the issue. Such problems tend to get ironed out over time, so Ubuntu 12.04 (or 12.10, should you care to upgrade again) may be better on this score than whatever you've tried in the past. Booting in EFI mode will enable you to eliminate the flaky hybrid MBR that you're presumably using now.