I went to a camera store today and looked through the viewfinder of their floor model using my same 180 mm f/3.5 lens. I was able to see the same little donuts at the center of the defocused highlights. Also, I have posted my question in the dpreview forum, and one person affirmed seeing the same thing. Although it constitutes a pretty small sample size, I'm pretty comfortable concluding that this is just what you have to expect with the 6D.
I also looked through the viewfinder of the 5D Mk III in the store, and the bokeh looked distinctly smoother, without the donuts. Michael Clark's explanation that this may be caused by the mirror design makes a lot of sense to me, although I don't have the resources to know for sure if this is the explanation. Some folks in the dpreview forum seemed to agree. Anyway, the mirror or whatever part of the design seems to be different in the 5D Mk III.
EDIT: a few days later and I've gotten delivery of a Canon Eg-S focusing screen. I believe it totally solves the problem! My 6D viewfinder now seems to provide a WYSIWYG experience.
Here is a photo of the Eg-A II screen (the one that I was in the camera by default and which I removed). When you hold it at arm's length, this psychedelic pattern appears. I think it's now pretty clear where the donuts were coming from--this seems to be the Platonic ideal of the donuts I saw replicated in the bright spots in the blur. The Eg-S shows a similar pattern, but there doesn't seem to be nearly so much of a dark ring in it.