What NPM did really provoked lots of developers. On their Privacy Policy page they state:
Acceptable Use - You will not submit any content that is illegal, offensive, or otherwise harmful. You will not submit any content in violation of law, infringing the intellectual property rights of others, violating the privacy or other rights of others, or in violation of any agreement with a third party.
and
You will not violate any applicable law.
This means that if Kik's lawyer did provide a prove that the name Kik is trademarked, NPM had the full right to remove the package.
This is pretty logical - the lawyer strikes high. Imagine NPM involved in a law case. This could lead to a lot of trouble and trust issues for the whole NodeJS ecosystem.
This rises another question - What will NPM's next move be? npm packages like google, yahoo, apple, trello, basecamp, etc. can be found on their registry.
What about express. There is a company named Express, founded in 1980, way back before JavaScript and NodeJS. What if they decide to take the act of removing expressjs, because of its name?
It may never (and probably won't) happen, but the possibility of this happening is somewhat concerning.
Update: @aniforprez clarified in his answer that NPM changed kik's ownership, where I though that npm removed the whole package (reference here). This still leaves the question of why NPM took such a drastic measure.