As mentioned, explosives. And flamers. And maces. And hammers. And cattle prods. Kind of in that order.
Killing plenty of other people beforehand does wonders, because flamers can and do hit their morale pretty hard (and the AI tends to "bottle up" around flames). As soon as it's low enough, you get a free turn or two as they drop and pick up weapons. Being on fire also goes through armour for free, for 5-10 damage. Worthwhile hitting them with 1-2 bursts of it a turn, until they're on fire and/or panicking.
Maces reduce armour, and 40-50 strength gals often get some damage through (at lowish TUs per swing).
Hammers are slow, but they hit hard enough to crack armour. Very hard in fact.
Prods still do 70 damage. Even if it's stun damage, it's often enough to go straight through. They're slow too, but you'll have a few laying around, or being carried, somewhere.
Assault Cannons w/Exploding Cannonballs are still 60 damage, and hit bottom armour within 3 spaces if they hit close enough. 80 damage with Steel Balls basic can still pip them.
Panzerfausts, Mortars, etc, all do more than enough damage to crack that armour, and are buyable from the start. Having 2-3 Panzerfausts is a reasonable thing to carry on the Bonny, just in case. Even Heavy Machineguns can do a bit if they're close and they've got sighting on the enemy (even if I don't actually like the weapon, you can spray and pray). RPGs tend to be early game too. About 35-40 damage+ is your minimum on it being worthwhile to fire at them, otherwise just smoke/bomb/grenade/molotov with that gal. Or smoke and bring out the cattleprod for next turn. 40'ish damage has a ~25% chance of doing something on a hit from behind, so don't rely on it, but it all stacks up. It scales nicely from there.
Smoke grenades do cause a bit of stun damage, and as fatal wounds/damage ticks them down, a barrage of them thrown accurately can actually do a bit. You're going to have some ready to go, and it's better than getting hit by heavy plasma AoE on gals that aren't outfitted to go through heavy armor. Smoke the area, or pile on some potential "damage ticks" through smoke grenades. I have no idea if it counts as "damage" for morale knockdown/panic purposes, but damage is usually damage, and does all that. 50-150% should count on under armour at their feet on stun, maybe with morale tick-down. Very theoretical, so it's best to use smoke to blind rather than stun them.
Remember the 0-200% damage of normal weapons, and the 50-150% of explosives. Everything counts in large doses, just so that you don't get entirely RNG screwed. Even a Linux SMG from behind will crack through occasionally, and a Boarding Gun at point-blank range from behind (or hand cannon at worst) has it even easier. The morale hit and fatal wounds will all add to the Marsec a'hole's problems in life. You can only rely on averages, so average the f*ck out of him.
50 health ain't that much, when you can pop smoke around him and keep averaging him. Having just 45 TUs turn them into statues if they can't see you, or spend most of their TUs trying to, to the point that they can't shoot that horrible, big, plasma, explodey thingy. It makes it less likely that they'll react as you run around behind them too. 20 square nightvision is scary, but only because it's as good as your gals'. Even through smoke, that normally chops enemy vision down. If your gal couldn't run, had 45TUs, and a weapon that took 16-18 TUs to fire (sometimes more), you'd hate smoke or anything fast moving around. Even with awesome armour. Approach it like that. Contain and destroy. But know their power, as well as their weaknesses.
They're hard, but they can be killed with "basic" weapons. Don't expect to go 1-on-1 with them until later. At the start they're an "all-hands-on-deck" proposal. Or smoke and run and smoke again. Until you can average them with enough gals to count.
(this is just "initial weapons" advice. Marsec Security are scary early on, but that's why I advise a good array of high damage weapons early on, regardless of accuracy or standard-use. You never want to come across something that you can't hurt)
