I have updated CPAN that way and it has always worked for me... I only use (perl -MCPAN -e shell) if I am doing a new Linux install. If I were you and it messed up before I would just read everything it says as it installs. Don't just keep hitting enter and accepting the defaults for everything. I normally install cpan modules directly from the source. It's very easy.

save the source
wget http://mirror/path.to.source/CPANsource.tar.gz
# tar zxvf CPANsource.tar.gz
# cd CPANsource
# make
(Get mad if I don't have the dependencies and wish I was using the cpan script ;-)
# make test
(Get mad if it doesn't pass the tests)
# make install
Note: you have to be root prior to make install.