It totally depends on the map:
- on summervillages f.e. all you need to do is use the tank and get dialed in on the flag - any kind of fast movement or sound (there's a clear manta sound 0,2 secs before the runner tries to snatch the flag) you hit the flag - boom, done. You need really good focus for this and 1 or 2 constant healers.
- on edgeclassic using the tank also helps a lot, but even a regular defence (like I do) just focusing on both sides and using the shock balls or beam can stop several manta runs
- on noname a well placed focused bender can stop 90% of the attacks easily
Generally using avrils is a good strategy if the mantarunner has to do a long distance run and the avril has time to hit him, so generally some big maps or maps where the runner has a long distance to go
There are also maps like Bloodbath where it's really hard to stop a well performed manta run, but that run is hard to pull off