So, figured it out:
The cursor blink period is controlled by a hard-coded value in
Resources/app/src/cursor-view.js inside the app package (right click Atom.app, 'Show Package Contents').
The culprit is on line 27:
CursorView.blinkPeriod = 800;
(default blink rate on OSX is 1000ms)
I'm currently digging around in the
atom.config stuff to see if there's a good way to set this in config.cson...
Update: As far as I can tell, there's no way to set this via config. Editing
cursor-view.js with your desired value and restarting Atom works, though.