Have each enemy structure keep track of whether or not it has been queued for capture by a given player so that that player's units do not attack it.
The Capture mechanic is a very cool part of BAR, but manually setting "Hold Fire" on the commander just to capture a metal extractor without taking it to half hp seems unnecessary. There are also situations where capturing enemy units would be a lot more viable if your own units would immediately stop firing at the unit that has been queued for capture.
Gameplay
It is very important to not end up with a "poisoned state" where an enemy unit is marked for capture but is not actually in a capture queue. One way to solve this is to keep track which unit has the capture-marked unit in its queue and then each time the capture-marked unit would be targeted, ensure that the unit attempting to capture it is indeed still trying to capture it. Of course, with giving commanders to teammates and with decoy commanders being able to capture, this would have to be a list of capturers.
Also, this probably shouldn't propogate through to teammates because of easy trolling.