No, Gemnasium doesn't to write to your repos unless you enable the auto-update feature.
To track the dependencies of your project, Gemnasium simply browses through your repos and downloads the dependency files that are supported. There's no need to write anything.
Gemnasium writes to your repo if you enable the auto-update and the pull requests simultaneously. It creates new commits and branches with the new dependency files the auto-update results in.