Thanks Noel for elaborating on your thinking.
It's necessary to stop and restart playback in order to get Melodyned clips to play back at the right time. Resetting the audio engine is also usually a good idea when there are stability questions, as for example when using plugins with a lot of latency. As a result, it's rare that I would want to click somewhere during playback and have the time jump there. In the use case described, I generally prefer to stop playback using the space bar, set the now time before the peak in question, then restart playback while looking at the relevant meters or other screen elements.
I think ctrl-clicking as a way to change the now time during playback seems like it might occasionally be useful for me, and it would solve the use case you described, without creating the possibility of accidentally changing the playback position, so that seems like a good solution to all of the concerns people have mentioned.
Also, I'm not sure that this behavior was noted in the release notes. I think that the surprise and mystification I felt after updating and having the playback position jump around unexpectedly would have been significantly ameliorated by a big boldface notice of what is a fairly important change in the behavior of the software.