The opening is flippant, true. But it's making fun of the police at least as much as the hippies (probably more).

Then you quote the possibly the most pro-government line in the whole piece, ignoring:
"But raw milk in particular has drawn a lot of regulatory scrutiny, largely because the politically powerful dairy industry has pressed the government to act."
and
""This is about control and profit, not our health," said Aajonus Vonderplanitz, co-founder of Rawesome Foods. "How can we not have the freedom to choose what we eat?""

As for the actual players, neither really comes out looking clean. The Rawsome owners appear to be trying to do an end-run around a licensing system:
"It is legal for licensed dairies to sell raw milk at retail outlets in California and 10 other states, according to research by the National Conference of State Legislatures. "
Licensing isn't exactly free-market niceness, but it's not a ban, either.

As for the government, you have police doing guns-drawn raids over licensing issues. Next thing we know, they'll need a SWAT team to issue parking tickets.

Which is a long way of saying I'm not really following your rhetoric.

For that matter, we don't force parents to vaccinate their children, for reasons that are no doubt stupid.

Whether they want to be or not. Safety Uber Alles!

While it's wise to be cautious of government, I suspect Neeser's quote was less about "we're the government, trust us" *Jedi hand wave* than about responding to the charge that it's The Man picking on the hippies at the behest of Big Milk. That meme was used very profitably by unscrupulous "dietary supplement" companies to avoid any oversight of their industry.

As for applauding the government, this is not about the government forbidding people from drinking raw milk; it's perfectly legal to buy and sell raw milk in California, provided you have the appropriate permits. Later in the LA Times article it's noted that the owners of Rawesome apparently thought they had a cute way to get around all those silly rules about running a "store".

Interestingly, it appears that other groceries catering to the faux-hippies stopped selling raw milk not because of The Man, but because of The Money. Specifically, because liability insurance was too expensive; in other words, the market decided that the potential costs from harm caused by drinking raw milk outweighed the profit of selling it.