I maintain a fork of a repo.
That repo which has been tracking a binary file (which is a sqlite3 file).
Every time I pull from that repo, I experience merge
I've released a tool that does what you're asking for. It uses a custom diff driver leveraging the sqlite projects tool 'sqldiff', UUIDs as primary keys, and leaves off the sqlite rowid. It is still in alpha so feedback is appreciated.
https://github.com/cannadayr/git-sqlite
You could define a custom merge driver specifying to always "keep theirs" (copy the version you are pulling) on top of your current version.
.gitattributes
mysqlite3.db merge=keepTheir
(That being said, remember binaries aren't always best managed with Git, especially if they are modified often)