Well I'm playing OpenXCom, I think that counts?
There is no difference that I know of in OpenXcom. The key point was that you're not playing a mod or with very customized settings.
The main problem seems to be that the Sectoids don't need LOS to be able to mind control half my squad in 1 turn.
The alien doing mind control don't need to get visual sighting itself on the unit to mind control them. It's enough that some alien unit has seen your guy at some point in the turn. The aliens also remember seeing your particular soldier for a certain number of turns (depending on alien race). The aliens have also seen you if they mind control one of your soldiers who then sees some others. Some aliens in non-vanilla also have "psiVision" where they can sense enemies certain number of tiles away regardless of walls. But that should not apply to vanilla.
That's why you'll need to adopt several techniques I described above. You'll need to avoid the aliens seeing you at all costs, keeping the distance, using a lot of proximity grenades, using smoke, and using tanks to spot the aliens if possible. Or if you need to scout with a soldier, do it with as few different soldiers as possible, and keep them separate from the rest of your troops. You'll also need to put the soldiers that can be seen in different compartments (e.g. different general stores rooms) so that if one of them is mind-controlled, the aliens don't get vision on the rest of them. And you can miitgate the effects of mind control by dropping your hand-held weapons at the end of each turn (and equipping the soldiers with a pre-primed smoke grenade, which they'll throw out first if they are controlled otherwise).
Sectoid base defense missions are by no means trivial nonetheless, but these techniques might make them at least more manageable and you should never lose in a few turns. Further, cyberdisks that accompany them can be very challenging if you don't have sufficiently strong weapons (especially explosives, using the battle tactics above).
