Liking the concept. I had an idea recently that might fit into the theme of this mod:
If a faction exists and it's blueprints are being used by another faction, cause a Nexerelin diplomatic event (if installed) between the two factions, and the faction sends a raid to retrieve it's blueprints from the planet/station. The raid should be tailored to retrieve the faction blueprints, and if successful then the blueprints should no longer be available for use by the target faction.
There are some other things that could be added to this, like allowing a faction to use blueprints if they have a high Nexerelin relationship (or player relationship).
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Editing to add that a decent workaround for military ships on the black market might be stability, where lower stability means more and higher quality (fewer d-mod) military ships for sale, in combination with the existing factors that determine amount and quality of ships available on the black market. There are a few neat things here, not least of which would be that destabilizing a world would be a really good way to get one's hands on that faction's ships.
Also, if you do Nexerelin integration, I could see a neat case where military ships end up on black markets nearby to the two warring factions, as a result of derelict ships being salvaged and repaired for sale.