If you're in ITB (or STB, I suppose - haven't tried it), you *can* take the turrets out when you first encounter them. (Personally, I think the new CTB mode is worthless - everything is about 10 times more difficult that way!) It just takes quite a while. I don't know if it's better to try and get past them and come back later or not, but it probably took me at least 2 or 3 hours to kill off all of the turrets in Preoria. My tactic was to crawl up behind crates on the first two and then each character would pop up, take one shot with a hunting rifle, and then go prone again. Alternatively, if there's a wall close by, you can have all of your characters line up so that they're one step out of the turret's view, and each turn you step in, fire, and then step back. And don't bother with burst mode against the turrets - it didn't seem to do any better damage on average than regular attacks, and it chew up ammo.
For those that are interested, you can get about 600 Fusion cells from each turret. But I'm now on to mission 11 or so, and I still haven't even found a weapon that requires fusion cells. It can just be a bit tricky getting past some of the turrets.
Eventually, you can deactivate the underground turrets, and the surface ones are supposed to activate. I don't know what happened, though, since the surface turrets never did anything. When I first deactivated the below ground turrets and it said the above ground turrets were active, I hit the switch again, and then one more time to reactivate the surface turrets. They never came up.
Anyone know how many HP the damn things have, because it takes a LONG time for each turret before they die. Something interesting is that some turrets you encounter around mission 8 or so (destroy super mutant generators) have something like 340 HP! Luckily, the same tactic still works, and by this time you should have a few people with sniper rifles, so you can actually damage them a bit.