You're on the right track. The way to bring the Borg into Trek again:
1) They are unstoppable. Starfleet can beat them on rare occasions, and only due to dumb luck. This means you can't afford to overuse them.
2) Assimilation is permanent, NO exceptions. No means NO!If the writers cannot maintain this degree of discipline, don't bring back the Borg at all.
3) Let the Borg permanently assimilate some beloved character. McCoy or Chekov would be the right level of gut-punch but probably be too radical. Gary Mitchell might not be high-profile enough. How about Pike?
Or Khan. Who's up for Borg Khan?
Hmmm, well actually ...
Lets see: While "unassimilating" Borg drones in the 24th C might be practical, it probably isn’t in the 23rd, thus satisfying your second requirement.
Maybe something like this: A Borg reconnaissance probe on a long range patrol picks up the signal from the Borg Sphere survivors earlier than anticipated and decides to take a look. They keep a low profile for awhile, gathering data, until encountering the Botany Bay. Recognising it won’t be missed and could provide sample specimens of the new species, they make the "mistake" of boarding it. Something in Khan's boosted immune system prevents their mental control ("dumb luck") and he turns the tables, using Borg augments and "slave units" for his own purposes.
A couple of military transports go missing near the neutral zone. The Enterprise is sent to investigate amid anti-Romulan diplomatic tensions. However the culprit is of course Khan flexing his muscles. A cat and mouse game develops. But Khan, who loses half his followers during a skirmish with a Cube carrier ship attempting to recover it's missing probe, becomes convinced of the Borg threat. An uneasy truce/alliance is forged to defeat the Cube (only possible due to Khans knowledge of their systems combined with Federation resources and perhaps using the probe as a Trojan Horse). The movie ends after heated arguments over whether Khan's group can become Federation citizens in some way or must be exiled.
You would probably need a more rational Khan whose antisocial behaviour was due to what he perceived as practical necessity, rather than an ego overload. Still, distrust would remain given his superior abilities and now technology, most of which he has retained, claiming facetiously that sharing it would violate the Prime Directive!
Whatever the plot, you get the horror of the Borg early on, combined with the potential of Khan's human frailty as a means of defeating him if necessary. Plus Khan is an individual character, something missing from the Borg.
As for point three: No, not McCoy! Anything but that!!
Well, the Borg could be delayed of course but if done as #2 or #3 and Khan keeps the Borg tech while being "safely shelved" afterwards, the way is left open for other unrelated stories to follow it.
You wouldn't think I'm not a fan of Khan or rehashed stories.
