Obviously the proper way to use such tools is to apply it only to articles claimed to have been written by "PJ", not to guest posts. And it's also key to remove paragraphs that consist of third-party quotes.
Concerning censorship, yes, you'll actually find that totalitarian regimes like the former German Democratic Republic formally allowed opposition parties and often even give them seats in parliament, but it's hand-picked opposition. Same thing with disagreements that Groklaw didn't censor:
What Groklaw liked best was dissent expressed in ridiculous ways. Those comments weren't censored because they served Groklaw's purpose of fabricating consensus.
What got censored instead were reasonable, perfectly polite, on-topic comments, or links to such material.