Yes, I believe so. It will depend on what your copy of MacPorts installs and how ports are currently named, but I believe that is correct, since it is the only GCC 4.7 installation listed. I think "mp" is short for MacPorts.
The MacPorts-based 4.7 version needs to be picked, since the Apple Xcode version of GCC is 4.2.1 and will not have the C++11 extensions needed to compile BEDOPS.
This document appears to describe a similar approach:
http://www.ficksworkshop.com/blog/14-coding/65-installing-gcc-on-macOnce you compile BEDOPS and run "make install", the binaries are put in a folder called "bin", located within your BEDOPS folder.
You would either copy the contents of this new bin folder to /usr/local/bin, or delete the precompiled BEDOPS v2.3 binaries installed in /usr/local/bin and then copy the contents of this new bin folder to another folder in your environment's PATH.
I recommend the first option. The first option would probably be easiest, but the second option may be cleaner, depending on how you have chosen to personalize your command-line environment.
In either case, I suggest having only one copy of the binaries, wherever they are put. If you copy the new binaries to /usr/local/bin, you will overwrite the precompiled binaries that currently do not work.
I do not have a BEDOPS uninstaller on hand for the OS X installer package, but I will add this as a to-do with the 2.4 release.