If the glue is standard cyanoacrylate ("super glue"), then, since the glue is moisture-activated, maybe you could do it without the nozzle getting clogged as long as you have some kind of amazing material for the nozzle that repels moisture.

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)?