I killed Tanova (undead matriarch) in chapter two when she asked me if I was part of the shadow thief guild. By doing so, will that prevent me from winning the game? (guesses are also beneficial)

nope. its just part of the game.

No and that's not the last you will see of her either, she is a vampire and must be killed in her lair but fear not she isn't as hard to kill the second time.