Alter Android Package Names for Free & Paid App Flavors in Git

I develop two versions of the same app: free and paid one. Both branches based on "master" branch in Git. Sometimes I merge master branch into "free" and "paid" branches to keep them up-to-date. But it is necessary for the free and payed apps to have different package names. Doesn't it confuse git commit history, or may be should I temporary rename package names before app buildings only and keep original package names in Git?