Since Eric and the rest of my team started working on the NTP code base in early 2015, we've eliminated over 50% of its vulnerabilities before they were disclosed simply by applying good software engineering practice where it hadn't been. In the year before my O'Reilly presentation, it was more like 80 or 85 percent. Everything we hadn't eliminated by disclosure or discovery time was fixed promptly.
There are other NTP protocol implementations besides NTP classic or NTPSec that are worth considering for some users. However, we felt that refactoring the reference implementation was necessary due to its use in many less-mainstream, but often highly-critical (in a life-critical or economically-critical or critical-to-scientific-research sense) applications. The non-NTP-related implementations don't always do what high speed trading houses need, or scientific installations built on aging but extremely precise equipment need, or controls system interfaces need, and on and on and on. We just didn't have a drop-in replacement available for all of the things that weren't web servers, workstations, and other commodity applications.
The "rift" article is now subscriber-only, so I can't respond there to its many inaccuracies (I was passed a PDF by someone who cached it, this is the only way I was able to read it). I was never contacted about it by the author, and I don't feel it was a fair treatment of the subject. That's okay. I learned a long time ago that fixing a mess will make some people thank you and some people angry with you. It wouldn't have become a mess by the time I found it if there weren't a cost to fixing it. People who fear controversy will have a hard time making a difference in the world.
I'm at work, but I'll do my best to answer any questions fired at me today on this thread. If there's something you want to know, ask!