well from what we knew about Frontier is was only of the few fleets that didn't allow cybernetics. So cyborgs being persecuted is unlikely if they're the majority. Don't forget a lot of older Zentradi war vets have implants as well (Mr. Bilier for example)
I figure the Vajra crystals will end up like the space whale meat in reactors. IE illegal but that won't keep some black markets opening up. Well that and provoking a Vajra hive is probably the fastest way to wipe out a system.
Fleets going rogue? Well i don't think they can really do anything about that. The tighter the yoke the more people will resist.
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