The ultimate goal is reproducible research: somebody else can easily take your project and recreate your results.
Git is a very useful tool for doing this with code. But it's not the only tool, and sometimes its the wrong tool. Like Mishabalyasin says, Git is the wrong tool for large data files. It stores compressed copies of files, with an additional copy each time the file changes.
You got it. If somebody can follow and reproduce your work by downloading your Git repo and a separate data file, then you've succeeded. Using version-controlled scripts to munge the data is a great practice.
If you've already committed the file and want to wipe it from your Git repo's history, you can remove every instance of it following the directions in the Pro Git guide: Removing a File from Every Commit. Note that you should make a back-up of your repo before trying this, in case something goes wrong.