Your question is equivalent to asking if you can edit a file before doing a git pull. The answer is yes, but if there are conflicts, then you will need to merge them.
Returning to your example, if there are no changes to your local configuration, then the files that
drush fu will write will be the same as the files currently in the repository. In this instance, git will happily do the pull, as it will consider the files to be unchanged, even if
drush fu rewrote them.
If you do have changes (
git status after
drush fu will show this), then it would be a good idea to run
git stash prior to
git pull. After you pull,
git stash pop will overlay your stashed changes on top of the pull, and you can see what the conflicts are.
Disclaimer: I have never hand-merged conflicts from features. I always pull the database from live to dev, and push code from dev to live to avoid this.