If you move your source into a subdirectory (many projects have a directory called src
for this) you shouldn't have any conflicts.
Your new repository structure might look something like this:
docs/
src/
content_scripts/
images/
libs/
ItemSelector.js
...
index.html (this is the existing file)
...
.gitignore
index.html (this is the new gh-pages file)
README.md