As a data point, I used a hop bag when I was extract brewing. It was a bit unorthodox, because I never went for a full boil, but I would heat the stuff up to between 80-90C, put in the hop bag for about 15 mins, and then pull it out.
There was no real protein issue to worry about, and the beers were clear. My goal was to hop up a standard kit (the last time I did this was on a Woodforde's Wherry kit). It made nice hoppy beers.
Using a hop bag???
With extracts, it's probably even better to use the bag, because it's otherwise quite clear and the hop chaff would muck up the beer. Now that I'm mashing, I boil loose and I don't really mind cleaning up the hops. They go in the compost (with the grain) which must make for some happy hopped-up critters. 
