Having been to a live event myself where they used the booths (MLG Raleigh), I can say that I don't really see why the booths would not be used. Fan experience? Really? I didn't feel like they detracted anything from it at all. I mean, the players are already up on a well-lit stage and are definitely a secondary focus (obviously the game feed on the screen is the main focus). If they were to have the players hidden from view entirely, that would be one thing. But I feel like as long as you can see them, that's all that is really needed. As a fan, I don't need to hear Zuna yelling at his team all game.
I kinda wonder if they didn't bother using them for the group stages while they're still playing in a smaller studio. It's what, a couple hundred people there in the live audience for these? Hopefully when they move to the larger venues for the actual bracket play, they will have the booths set up, because there will be many times more people in attendance, and it will be louder.
If they aren't using the booths, I would think that a 30-second or one-minute delay on what the audience and commentators see might help, too. It doesn't need to be the full 3 minutes that the spectator mode has, because nobody can communicate directly with the players while they're playing. It would delay the fan reactions just enough to de-sync it from the action that whatever was happening will already be done by the time the crowd reacts. The biggest downside to this is that the players reactions might give things away to the audience ahead of time. But this is far less of a concern than fans tipping players off simply by cheering.