Just as you'll constantly have a choice about whom to side with, so will you have different options available as you attempt to go about specific objectives. The main options involve force and stealth. In practice, you'll probably rely on a combination of these two elements. The game's manual asserts that "deadly force is always a choice, not a requirement" in the game, which means that it's theoretically possible to go through Invisible War without killing anybody. But that's like saying it's theoretically possible to finish the game in one sitting without ever saving your progress. Yes, you could do it if you really tried, but there's no reward for all that hardship, save for whatever personal satisfaction you'd gain from the accomplishment. In practice, you'll probably find yourself following a fairly obvious path of least resistance through Deus Ex: Invisible War.