You can set a custom merge driver in /etc/gitlab/gitlab.rb according to GitLab documentation.

gitaly['configuration'] = {
  # ...
  git: {
    # ...
    config: [
      # ...
      { key: "merge.ours.name", value: "Keep OUR version" },
      { key: "merge.ours.driver", value: "true" },
    ],
  },
}