You shouldn’t need to do that.
When the Gitlab CI runner runs, it only clones your blog git repo. It will not clone nested git submodules like a theme git repo unless you ask it to.
I prefer to not blend my theme and blog repos. That way I can independently maintain my theme and reuse it in multiple blogs.
Here is my Gitlab CI config: Files · master · Kaushal Modi / kaushalmodi.gitlab.io · GitLab
Here is the relevant piece from that that clones the theme:
# * Install my theme; need to first install git and then do git submodule update for that.
- apk add git
- git submodule init
- git submodule update --force
You also need a .gitmodules that points to the sub-modules: Files · master · Kaushal Modi / kaushalmodi.gitlab.io · GitLab