It would be great if you could try it and check that it works for you.
You can do that by:

rm -rf ~/.cache/guix/checkouts
git config --global core.autocrlf true
./pre-inst-env guix download --git \
https://git.savannah.gnu.org/git/shepherd.git

I did this and it worked!
I also checked if the downloaded files had any carriage return characters and they did not, so AFAICT that guarantees autocrlf was ignored.

thank you for this patch, I wasn't able to figure it out myself.

(I had to temporarily use my web-mail client which does not reply-all by default so I'm re-sending this message with reply-all, my bad)