It seems that the best approach to this is to achieve it via the data or a file based approach.
https://git-scm.com/book/en/v2/Git-Internals-Plumbing-and-Porcelain
I won't record the details here as I don't really know what I'm talking about, and I'm still little the wiser, so it won't help anyone for me to mislead them with the details of my answer.

In essence I've tried to make essentially deleting stuff a less naive and therefor more acceptable solution than it would have been when I first posed the question.