Yes, but discovering and proving interesting or useful facts requires some degree of transparency and replication. It's at least better, when possible, for a scientist to use apparatus whose functioning they can inspect, and that includes any major software components.

That's a bit different from Stallman's focus. Stallman is mainly interested in the freedom of users to modify the software they use (and share those modifications). But for scientific software the real issue is whether scientists can look at how it works. It would be fine for it to be under a "look but don't redistribute" proprietary license.