Right, at a minimum, the difference between the universe and the 'observable universe' is going to put limits on human reach, but maybe there are enough similarly minded organisms in the universe to overcome that.

The problem with an automaton based approach is what characteristics they would need to get the job done. To match the scale of altering the entire reachable universe, they would have to be self reproducing. To be able to prevent life from existing, given all of the different environments in the universe that could lead to the rise of life, and all of the different forms that life could take, they would have to be able to adapt to the local environment, and have enough complexity of information processing to be able to identify previously unanticipated forms of life, and find the best way to disrupt it.

At this point, you've, at the very least, severely blurred the lines of what life is, and most likely created a new form of life that is much more prevalent than naturally occurring life ever was.