Ah, must have just hit hot_threads at a slow time. It takes a snapshot of the currently running threads, so sometimes you can get unlucky and just hit it at an "idle" snapshot.
Given the number of fields going into doc values now, I think that's probably what we're seeing. Once you stop indexing, the CPU behavior should settle back down to idle (once the pending merges finish). The big spikes are likely a few large merges happening, while the lower background noise are smaller merges.
Note: the portions of the Definitive Guide that talk about Doc Values are relatively old...we wrote that way back at 1.0 when doc values were still pretty new and unoptimized. They've consistently improved since then, so I wouldn't worry about the overhead too much to be honest.
If you know this index will always be small and replaced consistently, you might consider disabling doc values...just with the caveat that the behavior might not last forever (e.g. when 3.0 rolls around). I believe the plans are to completely remove fielddata completely, so if you want aggregations you'll have to use them regardless.
But if some of them are never aggregated on at all (just for search), that'd be an easy win. And since the index is replaced frequently, you can always re-enable it in the future for those fields.