switching branches when they use different submodule remotes

I was confused earlier today when I switched branches in a repo with libgit2 in a submodule.

I knew that the different branches used different remotes for the submodule -- one remote is older, the other remote has newer 
development.

   git://github.com/pieter/libgit2.git
   git://repo.or.cz/libgit2.git

so when I switched I deleted the whole libgit2 dir and ran:

   git submodule init
   git submodule update

I was switching to the branch that referenced git://github.com/pieter/libgit2.git and
I was surprised the newer branch was cloned instead.

Looking at the doc for git submodule:

   http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html

it made it clear that executing init does not alter existing information in .git/config so I deleted the reference in 
./git/config manually and started over.

Is there a better way to handle this?