Do you have control of the surrounding area? This changes the tatics that can be emplyed to either capture or kill him.
No control, Take him out as soon as possible with the minimum damage to others.
Control, First you have backup troops cutting off access from the area. Next you have helicopters waiting a short distance away.Attempt a sniper shot when he is leaving the building. If this is unsuccessful deply the troops to surround the area. If this is not working call in the helicopters to complete the mission.
I have no formula for determining how many casualties, one casualty is too much. But the idea of letting him go to kill more innocent people would weigh heavily on my decision on when to act.