Nope. They weren't there to stop it, even they couldn't do that. They were there to prevent space faring life from interfering with their work, which was to move stars and planets around to avoid the extinction of life when the two galaxies DID collide (Andromeda and Milky Way specifically, which is actually going to collide with us). It was an interesting idea, although the wolves eventually failed when the greenfly emerged.
Alastair Reynolds in his Revelation Space books has a machine intelligence which killed technologically advanced races only (not primitive ones) because it had a massive engineering task to perform (stopping the collision of the Milky Way Galaxy with another galaxy in a hundred thousand years from wiping out all life) and it viewed space-faring civilisations as too short-sighted and an unpredictable risk to it's project.
Well, they considered the first humans they contacted to be drones. As their own species was primarily composed of drones which were controlled by the queen and thus weren't actually individuals.
Ender's Game had aliens with a hive mind, who considered killing a few humans as no more terrible than killing a few skin cells during a handshake.
Well, the Shadow and the Vorlons had different ideals about how life should evolve and grow. The shadows embraced struggle as the mechanism to cause a species to grow and advanced.
Babylon 5 had the Shadows, whose goal is not to kill all life but to strengthen it by weeding out the weak.