What this person is proposing is functionally similar to forms of anarchism and anarchist theory has some answers to these kinds of questions.

For example the communes could have a federation where representatives are sent to settle disputes. Likewise instead of a fixed 2000 people with walls between you could have people in several smaller overlapping communities which act as bridges across a network of communities. Similar to how a person can be a family member and a company employee and a resident of an apartment building etc.

Though I don’t completely buy in to everything it says, https://theanarchistlibrary.org/library/peter-gelderloos-anarchy-works goes into how anarchist communities can and have worked

we can just gently smooch the boots

He might have even had some dangerous written materials they should have searched his whole house. Or maybe dangerous chemicals hidden in his closet. Or maybe dangerous weapons stuffed in the couch cushions. They should have ransacked the whole place.

Why even endanger themselves going in with just cuffs? Flashbang the guy before he can react with a possibly deadly weapon. Drive a battering ram through his front door it only takes a second to open fire.

Put him under surveillance for a few weeks and collect his whole schedule so you can hit him when it’s safe.