I was discussing this a bit with some friends, and I came to a simple conclusion.
Base portals should be uncpaturable. If it's not a neutral portal, but a base portal, it should be uncapturable.
The ammount of time it takes to ninja a flag and lock, is a pretty small window. And yah, you can counter it. But Warscore, as a mechanic, is good enough. It gives you incentive to cap flags, and keep them, and it gives you a hell of a large advantage, for 'x' ammount of time once you hit priests, catas, and giants. The momentum you gain with priests allows you to push most base defenses down, and keeps retreating to a minimum. The cata advantage, finishes off those towers that still stand. So on, and so forth.
Momentum is hard, but not impossible, to halt or even reverse. But a successful sneak attack on a portal is very hard to come back from, because it further devides attention, and puts a lot more damage from the enemy team on the field, giving them a huge advantage. As if the advantage of controlling the flags and warscore, wasn't enough. The flip side to this coin, is that its also possible to come back, from a disadvantage, by capping portals and locking. If a team gets giants, but can't spawn any troops, and you can keep it that way, you will push them from your citadel, push to theirs, and win the game.
The fact is, end game, creeps are a powerful asset. Too powerful to be denied to one team, and granted the other. Having flags taken is detrimental in several ways, most of them obvious. What about the upgrades youve put into it for creeps? All that money is wasted if they can't spawn.
The worst part is, when you get a portal ganked, its virtually impossible (without multiple interrupts) to keep it from getting relocked, and relocked. Even if you guard it, the enemy has a great timer in the form of a cooldown, letting them know when it expires. If they are like me, they will warp to it as soon as they know it is about to expire, and start to replant immediatley, then cancel, to try and make the enemy guarding it waste their stun, then proceed to actually lock it. Worse still, most of the time, the citadel is being pounded so hard at this time that enemies will have to leave portals alone to get creeps off of it.
Thus came my conclusion. The lock is not overpowered. The ability to capture, and lock, base portals, IS a gamebreaking experience, and an overpowered strategy/move/whatever you wanna call it.
Perhaps my rush to say Portals shouldnt be capturable is extreme. But one thing is clear to me. At the very least, base portals should not be lockable by enemy teams. This would mean they have to baby sit the portal to keep it under their control, and divide their attention, as well as the enemies. This is a fair trade off, for the huge advantage gained by having an enemy portal. The ability to simply cap it, then return to smashing citadel or ensure your own creeps are living and stacking up, is too large an advantage.
Make them uncappable, or unlockable, and the game has a lot more leg to it. No longer would matches be determined as soon as you see that flag go red (cuz lets be honest, the chance of recovering from that is slim. Yah it can be done, and I've seen it done....but its usually more than just skill. It usually involves a mistake/carlessness by the enemy team and some luck).
I don't really see a disadvantage in terms of game play by having them either uncappable, or unlockable. It would simply remove a fire and forget tactic, that is too powerful. Those who argue that it isnt too powerful, I don't really understand. If it wasnt a game ender or a tactic that had great impact, none of us would bother with it....But as I said...end game creeps are a huge advantage. More of em, is more of an advantage. Warscore is something you have to gradually work at, and put a bit of thought behind, and quite a bit of effort, sacrificing levels at times to secure flags. But portal capping, is not nearly as strategic as some are making it out to be. But it is powerful. And it is the way we have adapted to playing the game...so its scarey, for some, to think beyond that, and look at the larger picture.