By the time a Hive Fleet has been called in, you're looking at 4th - 7th generation hybrids in large numbers, lots of purestrain Genestealers, a Brood Lord and maybe a Magus actually on the ground making trouble. Genestealer Cults are playing the long game, and can be found at any stage of their development. But only established cults that have revealed themselves would really warrant the attention of Space Marines. Anything less than that tends to be the domain of the Inquisition or local Imperial authorities to figure out.
Typically when the Genestealer Cult is fully realized, it's already brought most wings of government under its sway, or they are the first to be taken out when the uprising happens. So you could also include lots of citizenry and Planetary Defense Forces using actual imperial weaponry. The Genestealer Cult itself is largely an insurgency force. But what it can eventually take control of is an entire planet worth of armies and weaponry. Really a question of how complete their takeover was, how much the resistance cost them and what remains after the dust settles and the Space Marines arrive.
To be clear, I am planning for the long game, because Space Marine Chapters strike me as entities that should be very much about the long game. Before I'm done, I may switch to a pausable-tick system (a la Paradox titles), because I can imagine there being weeks that go by without anything interesting, and that could be a lot of button clicking. I don't want to hand-wave the training of entire new companies of space marines... I want the idea of sacrificing a squad to save a planet to be a painful acceptable loss. (Rather than either being so painful people savescrum around it or so trivial that people burn through space marines like they're IG.)
All of that to say: the idea that a GC uprising on a planet happening a 100 years after the start of the game, due to a single genestealer starting things off on turn 1... I totally want that to be a thing, and I want the 5,000-ish game turns required to get there to be something the game and player can both handle comfortably, while still allowing the time granularity to avoid the Civ-style "a battle takes a year" stuff.
From my recent (8th ed? 9th ed? I don't remember) research GC appear more often armed with mining equipment than anything else... probably at some point in the future, I'll care enough to try and tailor the armament of GC forces to the type of planet. For now, though, they'll all have the same types of squad loadouts.
When I get to requests in a release or so, my hope is to flesh out planetary and IG-Army leadership sufficiently that they occasionally send out general calls for assistance, or specific pleas to the player's chapter. That will sometimes include requests that seem more suited to an IG regiment or Inquisitor, because, hey, if Emperor's Children want to come solve the problem, instead, why not? And things I've seen in fluff, like the idea of a mining expedition at a planar pole accidentally deicing a carnifex that starts rampaging seems like a not unreasonable situation for calling in the Marines.
I also just like the narrative through line of something like "remember 50 years ago, when the governor of that planet sent out a request for investigation of several high-ranking generals disappearing, and we thought it beneath us to respond? Well, guess it must've been Lictors, because that planet is being overrun with Tyranid now, and the Guard forces on planet are being decimated... should we do something now?"