Free speech absolutists can still have opinions, criticize others, and choose who to associate with. They're not advocating for censorship or legal penalties for speech.
One can publicly declare a speaker to be a wrongheaded pig that all decent people should ignore, but that's a wholly different thing from ensuring that said pig is unable to utter its wrongheaded ideas in public.
What specifically is being done to persecute this hypothetical pig you refer to? As always, the details matter.
In regards to the Tor Project's public statement that is TFA, they've chosen to stop advertising with Mullvad [0] because they strongly disagree with specific political positions that a Mullvad co-founder has publicly endorsed. They're not backing out of working on the Mullvad Browser because they figure that stopping that work -and losing the new feature testbed and (presumably) the money they get from it- would hurt more people than the implicit endorsement that some folks will see by continuing to work with Mullvad.
[0] ...this is referred to as "proactive co-branding" and "joint promotional activity"...