I assume what he meant by Deus Ex having "too much freedom" is that Deus Ex, like a lot of old school CRPG, aimed to make huge portions of the game world interactive even if they served no purpose. Everything and the kitchen sink, in the most literal sense. And sometimes that made for some (though very welcome) goofy and amusing outcomes, even if they didn't fit contextually in the game world.
Dishonored doesn't seem to be going for that angle, so much as making everything in the game world relevant to the gameplay itself. Freedom is, after all, an illusion. One controlled by the designers and programmers. I feel that we're most disappointed by arguments of 'freedom' when a game fails to react in a way we expected it to. Like, invisible walls, or invincible characters, or over streamlining of a level. Anything that makes the designers intentions embarrassingly transparent, as they clearly want the level to play out in a certain way and it's now become obvious. Good game design, particularly in terms of game freedom, is less about "Look at all the crap I can interact with!", and more about giving the player an assortment of means to interact with the game world, and keeping that interaction consistent throughout. Like, if I have jump/teleport skills, then I always feel I can use these skills in logical and creative ways. If I can kill and trick NPCs, then I can do this with as many NPCs as I please. That the level and game design feels unrestricted because I never hit that wall of illusion where my skills and play style suddenly don't work for no apparent, logical reason.
