Another tip I have (not directly related to dealing with the Chargers): If you happen to cross the extract point while doing the main / secondary, it doesn't hurt to drop supplies and other any support stratagems there beforehand. You can also drop all the samples gathered at that point, so they will be waiting for the extracting time. It never hurts to plan ahead, so we are usually planning the mission route that crossing the extraction point will happen.

Doing this has in my expetience increased the chances of getting out with the all important samples, especially when the mission time is running out and the Super Destroyer leaves.