The real problem with Genestealer cults is that they infiltrate all parts of society. So, when they lead their eventual uprising, it's not just random people with random weapons, entire military regiments can suddenly be taking over. This is shown via the Brood Brother rules coming in the Genestealer Cult codex for 40k. Get a look at how they work in this preview.
From the article:
Once a Genestealer Cult has gained a solid foothold on an unsuspecting world, the planet’s own defenders become tempting targets ripe for indoctrination. Known as Brood Brothers, the cult faithful who infest loyal Astra Militarum forces can uproot the entire chain of command when the order arrives, adding highly trained, better-equipped fighting forces to an uprising.
Codex: Genestealer Cults arrives for pre-order this Saturday, along with updated rules for adding Brood Brothers to your army. These represent local forces that have been subverted by the Patriarch’s will* and they add some tactical flexibility to your army. Need some expendable troops to claim an objective? A Brood Brothers squad is ideal. Want some more mobile firepower? Try the Scout Sentinel.
You can include an entire Detachment from Codex: Astra Militarum in your Genestealer Cults army. Not only does this give you access to lots of additional units but, even better, it doesn’t prevent the Genestealer Cult units from using the awesome new Crossfire rule to gun down anyone standing in the way of your rebellion.