It’s being repeated over and over again that you have to protect your trademark or else you lose it. This is true, you have to protect it …. within reason, and within the scope in which your trademark applies.
Kik Messenger has a trademark that covers audio/text/video messaging. 
Kik Textile has a trademark that covers textile and apparel. 
Robert Baker apparently has a trademark on Kik that covers only caps and t-shirts. 
Azer Koçulu just wanted to write a software to ‘bootstrap and kickstart your next project’. He could apply for and probably receive a trademark for Kik in the field of “software code generators and programmer productivity tools”.
In a perfect world, I feel that what NPM should have done is step back from the situation and say that if a company wants to claim a trademark violation, and there’s any level of ambiguity, then they should file an injunction within the legal system. Package registries should be neutral 3rd parties, and not opinionated.
However, I don’t blame NPM for ducking away tail between their legs. Trademark disputes are messy. Even if you are utterly and obviously in the right, an obstinate company can drag it out for decades.