Purism put their microcode (and its updates) to the Coreboot, which is already non-free. Their OS stays free and FSF-endorsed. Thanks to this, I don’t need to have non-free binaries in my Qubes installation. I wish I knew precisely how to get rid of them all.
The microcode issue is not as straightforward as you seem to imply: You have to choose between freedom and security here, a choice forced by unethical corporations. This is like a choice between Linux and MacOS, assuming the latter is more secure. Not very simple choice and shouldn’t be necessary… Also, I believe that true security is impossible without freedom and ownership of your hardware.