How to save soldiers mind controlled by the warlock in Xcom 2 war of the chosen?

Solution 1:

If keeping the Reaper alive is your only priority, then simply EVAC the remaining soldiers as quickly as you can. This will fail the mission, costing you that Resistance contact… but Elena will live. Given the situation you described, the mission is probably a lost cause anyway.

If you have one soldier left that is MC'd by the Warlock, then the mission will immediately fail with them being Captured. I know this from when I was doing the Codex Brain Coordinates mission with a single soldier. I'm not sure if this stays the same for retaliation strikes, but the objectives are fairly similar so you should be good.

After the mission, you can locate them through the Resistance Ring (with L2 bondmates if possible) as soon as your current covert action is finished, and then mount a rescue.

This has the following additional side effects; I really don't believe in a true "nothing else matters" scenario unless you have an Instant-Win Condition or are faced with a game over if you fail:

• The Warlock may gain some additional knowledge on XCOM's operations.
• You might need to do a mission or two without her. But, you should be used to this.

Solution 2:

If she happens to have a bondmate that is at the rank 2 bond (or higher) on the mission, you can move him/her next to Elena to cleanse the effect.

Other than that, there is no way of removing the mind control short of killing the chosen or killing the resistance soldiers and waiting for it to wear off.