That certainly reads to me as an attempt to be colloquially amicable. Certainly it would have put a better foot forward if he had started with something more like "We are trying to do the right thing and...", but minor self-effacing obscenities are something we Americans tend to use in a colloquial, "buddy buddy" way to suggest that we are aware of the complexities of the situation and empathize with the other person's plight and how they must see us. It certainly read amicably to me, but I can also see why it may not read that way to others, especially with out vocal pattern contextual information, and that it may in fact only add to the confusion of the resulting conversation.
(Thinking about it, I wonder if this is something of an l10n/i18n issue... Oh the wonders of global communications and how it can break down.)
The whole thing reads to me as a cultural misunderstanding. At least, I wouldn't consider the Kik messages to be be anywhere near appropriate language or tone. Given that npm seemed to be fine with it, I guessed that it's not unacceptable to American ears, but my emotional reaction probably would have been along the same lines as the original author.
NPM should not have been fine with it [0]. KIK|Bob's language is in violation of npm's stated Code of Conduct and Dispute Resolution process. If npm actually read KIK|Bob's emails that were sent to Azer, I don't see how they could have allowed that dispute to continue, let alone side with KIK|Bob.