What about giving it a negative anti-matter recharge rate from a passive ability? Then just make the cooldown long enought that by the time the ability is ready to cast again there is no anti-matter left. The problem would be that it would only be one use ever, regardless of another player capturing it. The solution would be to have all of the structures anti-mater restored when it is captured(maybe make that a secondary effect of what every ability you use to capture it, with a delay so that the anti-matter is only restored after the structure is captured.
One problem with the above is that there are anti-matter restoring units, so the anti-matter would need to be above anything a player could do. Say 10000 anti-matter for the structure, ability costs 9500 with a 10 second plus cool down, a passive ability that drains 100+ a second, and have the ability auto-cast as soon as it can.
You would have: capture-> anti-matter restored -> ability auto-casts -> anti-matter zero by the time the ability is ready to cast again.
