What I suggest is very simple: Add a few recipes:
Red/yellow Flower in Exctractor = more dye that what you could obtain by crafting grid.
Of course, it would only works with "Raw" dye: you could get more dye by this way instead of the crafting, but it wouldn't works with lapis/Ink bag.
(So, basically, Cactus and flower, maybe more with mods like RP2)
PS: I thought someone had obviously already suggest it, but I did not find it.
If you have found it, post it in replies.