Does choosing to complete optional missions affect the level of Chaos in the city?

I have just gotten a mission from Granny Rags to poison the Bottle Street Gang's black market elixir with the guts of a diseased rat, which will cause anyone who drinks the mixture to develop the plague.

This does not sound like a good idea.

However, the Outsider seems to trust Granny Rags, and I feel like I ought to trust the Outsider, considering he gave me magic powers and all. But I really don't feel that poisoning the innocent citizens who buy the elixir is something that my Empress would condone.

Then again, it might be that the game is like Mass Effect, and ALL side missions are beneficial in some way or another, no matter how suspicious the character providing the mission seems to act. I feel uncomfortable trusting my ability to metagame, though...lives are in my hands!

Are there any optional missions which I should NOT complete if I want to minimize the amount of Chaos in the city?

In general, the optional missions that you should not complete are fairly obvious.

Specifically, you are correct, and the Granny Rags mission does increase Chaos. The Outsider is not specifically determined to keep it at a minimum, so his endorsement does not help in this regard. The Bottle Gang is helping to keep the plague at a minimum by selling their cheaper version of the Elixir; indeed, in a later mission you find a note that seems to indicate that even the guards use it if something happens to their ration. After you taint their stash, you spread the rat plague until they figure out what's going on, and the source of cheap Elixir is gone.