Forking is healthy. In the late 90s/early 00s, you'd hear about a new Linux fork almost every other month. Those forks would die quickly, but sometimes would have something to contribute back to the larger distros.

The fact that Node is popular enough to fork is a good thing. There is an inherent disagreement between Joylent and the Io.js folks, not on technology but process, and it's likely that the conflict will be resolved that way they always are (the more suited fork will win out). The risk of fragmentation is very low.