I’ve implemented something similar recently where add-on updates/deletions are deferred to the next startup. This actually required bundling an executable to restart Anki (something similar to @Shigeyuki’s AnkiRestart add-on), delete/update the add-on and launch Anki again. I’ve been thinking of a general approach suitable for contribution to Anki.
Starting from this post would be good maybe? Bundling Numpy in an add-on - #3