Comment 4 for bug 805717

you should be able to run a decoupled mono, but you should make sure it does not install anything into folders controlled by the package manager (/usr/lib/, /usr/bin, ... ). Commonly used folders which are save are e.g. /usr/local, /opt/, /srv or your home folder.
when building from source the installation folder is usually set with ./configure --prefix=/folder/mono
If the installation has problems finding the libraries you may have to set the MONO_PATH environment variable to tell the runtime where the newer libraries are.

Security updates are backported to the stable releases of debian and ubuntu if the issue is severe enough.