Is using Helicopter or Dragonfly really that risky? I killed all cults by'98 using the helicopter, the only one that gave me issues iirc was either the Black Lotus or Red Dawn, the rest were pretty easy, using Blackops weapons and Liquidator Armour.
I suppose you have played with a lower difficulty. First two difficulties only have about 1/3 of the enemy numbers that superhuman has, for instance. Yet even with the lower difficulties I still suppose it is risky and may require save/reloads. With SH forward bases have about 60 enemies and HQs 100+ enemies.
With vanilla X-COM AI mechanics it would certainly be doable at least with a good spawn location. But X-Com Files has 'spotter' and 'sniper' mechanic, which will mean that dozens of enemies can come at you and shoot, throw grenades or use grenade launchers blindly at you if you hit one of the 'spotters' (most of them are, except with BL), even if you stay inside the smoke or the cover of darkness (so they can't see you). Grenades and launchers are usually the most destructive part.
The most effective way to counter this AI mechanic is to go there at night (and hope there are no enemies nearby spotting you), throw out flares and throw grenades for the first 5-10 turns or so, and not shoot at all. Throwing grenades does not trigger "sniper backfiring". But being able throw sufficient number of grenades requires a significant number of agents (you will also have to throw flares, many grenades will miss and many enemies require multiple grenades; nearby ones can be dealt with dynamites, which take more space and are heavier, so you'll need more agents for that reason as well).