You "own" a tower when the flag disappears from the top, but it's not ownership in the sense of RTW where it will fire at the enemy. You're just turning it off so it doesn't shoot at your men.

And the dynamic for this is different too. You have to clear all the enemy units near the tower, not just on the walls but also at the base of the walls and nearby streets. You can't just run troops through the tower to turn it off, if there are still enemy units anywhere nearby. Anyway, check for a flag on the tower. If there's a flag there, it's still shooting at you.