Maybe a simpler approach would be to extrude through a mask that has a grid-like pattern of holes? Obviously you could only make isolated dots of glue, but not overlapping lines of glue (you can't have floating islands in your mask layer). So although it wasn't the technique used in this article, I guess it could work just as well, right?
[1] http://equipment.loctite.com/productLineDetail.cfm?pl=21
[2] http://www.youtube.com/watch?v=q4RR67d8CC8 (larger epoxy extruder, same idea)
Maybe someone with experience using cyanoacrylate in industrial settings can speak to this. All I know is that my hobby-store super glue nozzles (cheap plastic) get clogged almost instantly. :P
http://en.wikipedia.org/wiki/Cyanoacrylate
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But, my main concern with any kind of XY gantry (as in an inkjet printer like you describe), is that it would take frigging FOREVER. There's no way you want this glueing step to take 45 seconds per unit or more. That's the puzzle, I think, is how did they create this glue grid so quickly that it rivals the blob approach (1 - 2 seconds)?