No, you're just misinterpreting it.
The "active" part is when the counter can reach out and grab the opponent. The recovery is after that, but before he can do anything else. However, he's invincible throughout the entire thing.
If this wasn't true, you wouldn't be able to 6D or 2D through Nu's sword super, since you would get hit out of it before you could do another counter. But since you're invincible all the way through, you can do another counter as soon as you recover and never actually enter a state where you can be hit.
http://www.youtube.com/watch?v=MLX4uZIB0rM#t=0m38s
And during this entire time the opponent will get caught by the counter if they come near it.