Turn off the BOMB option. (Byte Order Mark Bytes)
It adds two bytes to the beginning of a text file to indicate endianness. They are 0xFF & 0xFE, I forget which order is what, but that's why your VCS thinks your .vimrc is a binary file.
You should edit your .vimrc, then turn OFF the bomb option and save .vimrc. This should remove the BOM bytes. Worst case, reset/remove the BOMB option from your .vimrc file, then use vim's binary mode to remove the icky bytes.
# edit .vimrc
$ vim .vimrc
# remove / comment out the set BOMB line
# reset the BOMB option (:set nobomb)
# save file, exit vim
If the BOM bytes are gone (use file), you're done, commit and enjoy. If not:
# remove the BOMB bytes using binary mode
$ vim -b .vimrc
# save and exit, .vimrc should no longer have the BOMB bytes.
Also, the 'file' command can tell you if a file has the BOMB bytes too.
You can also use the 'xxd' command (comes with vim) to view the hex bytes of a file:
xxd .vimrc | head
should show you if the BOM bytes exist or not. (It's quite handy for many things)