Merges always create new commits (except in the fast-forward case), so merging into an old commit isn't possible without creating a new branch or rewriting the existing branch. If you want the database dumps in your master branch you need to merge into the tip of the master branch and deal with how gitk looks.
Other options to attack the long-lived parallel branch:
- Have the database dumper commit directly to master.
- Unless updates are very frequent, have the dumper create a short-lived new branch for each dump.