Yes, but this is not particularly a problem with rEFIt, it's intrinsic to the way firmware password and admin access relate to each other -- if you have either one, you can take control of the other. For instance, if you have admin access, you can disable or change the firmware password with nvram command, You can also change the boot volume with System Preferences, effectively bypassing the firmware password protection.
Basically, the firmware password is there to protect the integrity of the computer until the OS starts and can start enforcing its idea of access controls, at which point admin passwords are the relevant control. Don't think of firmware password as a higher-level control, it's more of a supplement.
Boot from an install DVD or USB key (If you have one).
From the first installer page choose Disk Utility from the Tools menu.
Check to see if it finds your partition.
Verify/Repair it.
Then, from Tools, choose Startup Disk, and see if you can set your system partition.
If you don't have an install DVD or USB key there are plenty of instructions around on how to do it.
iPartition can change partition schemes without wiping the disk if it comes to that. It's a great tool to have, I've used it a lot for various disk activities over the years, with Linux, Windows, and OSX partitions.
You need a GUID disk to boot OSX normally, not sure how you had it working with an MBR. Disk Utility will normally tell you what you have and how to correct it, if it can.
This is similar: HD accidentally reformatted to MBR, how to get back to GUID?
Long story short - make sure you back up your disk, you're probably going to be reformatting it.
Best Answer
Installing a firmware password will prevent anyone without the password from selecting a different boot disk to start up the computer. It will also disable some startup key sequences, like getting into single-user mode. I don't know how the firmware password interacts with something like rEFIt.
However, if someone can open your computer, they can disable the firmware password by pulling one of the sticks of RAM and/or just access your hard drive directly and do what they want with it.