There is no contradiction in saying that value judgments are relevant to what value neutral facts we want to unearth. Deciding which science to study and research does require a value judgment, but this judgment is about a body of factual discourse and is not part of that discourse. In blurring the distinction here there may have been something of an assimilation of the language of scientific observation and theory to language about science. A metaphysical realist will surely reject this assimilation. Moreover I agree with Putnam that aesthetic considerations play a role in the methodology of science.
Physicists often look for symmetries, and there is aesthetic motivation here.
Also, however, they can be influenced by the consideration that in the past the search for symmetries has been successful. Two or three hundred years ago this heuristics may have been influenced by theological considerations to the effect that God would have created a beautiful universe but now the experience of the success of the heuristics can be enough to encourage us. However the methodology is one thing, truth another. Theories have to be tested by facts. We rejoice when the heuristics of seeking symmetries succeeds.