Some should cool down.
I am using Pillar to write my (internal) docs.
And I use markdown too.
Both have their uses.
Compared to things like RMarkdown, knitr, and RPubs in the R community, what we do have is passable in terms of output. We have a small community, we have to deal with that fact.
I hate the figures not going where I want due to the LaTeX generation in Pillar.
As for class comments, markdown would make more sense to use when putting files under source control on git and then stored in github because filetree generates README.md files for such comments.
It makes for a nice reading there. In that respect, Pillar class comments will be more of a nuisance than a help.
For generating web documentation, it is easier to provide markdown so that any web framework will be able to convert (e;g; Showdown.js and 2 lines of code).
Furthermore, a lot of Pillar files embed non pillar markup for special things.
For me, Pillar is for the books. And speciality applications that use the visitors to produce other stuff (among which Markdown).
As for writing stuff, I do md and pillar files in Vim. So much for specific tools that weren't satisfying when writing. Too slow, too cumbersome, not enough power for editing (compared to Vim, yeah, nothing comes close in terms of speed once you know the tricks).
Phil