The main problem I see with phragmites so far is that it is very agressive. Too much of anything, too fast, can throw off the ecological balance.
After I made this post, I did an engine search and found a blurb on the Pine Barrens Enthusiast website about removing the reed in Wharton State Forest. The blurb was from least year and the call was to help remove Phragmite seeds and cut them back in the spring. It was in a small area of Wharton. I see the Audubon author's point about management of phragmites but not eradication, and that plans to deal with the reed should be made on a case by case basis. In some cases the growth of phragmites may need to be slowed down, and perhaps is some cases, completely removed from an area. As the autubon article points out, a reed dominated marsh has the same amount of biomass as an equivilent marsh dominated by the other species (I forget the name of its "competitor").
In any case, if phragmites growth gets out of hand I think there is a problem. Too much growth can choke a marsh, not allowing water to flow through it and it could even dry up faster than it would. Ecological succession could be put on fast forward.
I wonder if the phragmites removal project is a yearly thing or was just a one-time deal, or if it is done as needed. Maybe we Pine Barren Enthusiasts could look into that. If I stop by the Wharton Forest ranger station I'll have to ask about it. Or maybe they can be contacted via other means.
One more thing. The Audubon Society perspective is from what the reeds do for the birds. This, of course, is important. But, like any other subject in the Pine Barrens, it should be addressed from other perspectives.