I've been following this and other 10.9.x NTP discussions for a couple months, and I've felt the same frustration. I've attempted many fixes, trying to use as much of the existing OS components as possible. I found no way to make the the 10.9.x ntpd work, and decided to directly use ntp.org's distribution. Moreover, pacemaker was unsalvageable and provides no value to me, so I've disabled it. Yes, I understand why Apple created pacemaker and hobbled ntpd, but the Mavericks NTP ecosystem Is simply broken.
The solution that works for me, which I strongly recommend, isn't trivial: unload pacemaker, download/build/install a clean copy of ntpd, modify /usr/libexec/ntp-wrapper to use the new ntpd, manually update /etc/ntp.conf. I have had three Macs running smoothly with this set of changes for weeks so I'm very comfortable recommending this approach.
I'd much prefer an Apple solution, but seeing as 10.9.2 didn't fix the core problem, I've taken matters into my own hands. FWIW, 10.9.2 did address a minor issue with ntp-wrapper not correctly parsing ntp.conf server entries.
Sorry to link outside of This forum, but I've tried to give more details here: https://atmythoughts-v2.squarespace.com/living-in-a-tech-family-blog/2014/2/28/w hat-time-is-it.