Git: Prevent another crash on checkout

Crash happens if the repository has a submodule with local
changes that requires updating (commit changed between current
branch and new branch)

Since we already refresh for every repo change, just add "expect"
for checkout and remove the code accessing the deleted index.

Change-Id: Ic464129a2f001e017244fdf719b282dcbd9dffa4
Reviewed-by: Tobias Hunger <tobias.hunger@digia.com>