I've been considering this situation a bit more, and have come to the conclusion that my concern is the following:
I dislike removing something from crafting (that removes DEPTH, making it a shallower play experience), without something additional being added that could create more depth.
I will admit the current dyeing system DOES NOT add this hoped for depth. The dyed item recipes seeming purpose is to be restrictive rather than creative. Further, the need to stock large varieties of dyes, dyed cloth, dyed leather, dyed clothing parts, etc is a terrible burden on the inventories.
However, the POSSIBILITIES of the dyeing system seem fantastic. And it's the loss of the possibility of what the current system could become that I mourn, not the current system itself. The sheer craziness of making a velveteen shirt with different front/back/sleeve colors makes me weep (and yes, a lot of people could end up look like clowns).
In addition to the possibilities I've already mentioned (redyeing to the current basic colors, and custom dyeing performed by crafters), I can foresee other possibilities. Perhaps, in the end, the burden of all of the extra custom-colored clothing would be to great of a burden to the item system (although I have my doubts, seeing all the NPCs standing around in their fancy gear).
If the materia system is added, and adds a great deal of depth to the crafting system, both with adding slots / slot-links to gear, plus the making and/or slotting of materia itself, this could easily add enough depth to compensate for the removal of the "dyeing at craft-time" system we have currently.
Other proposals for dyeing:
All gear is created white/uncolored. After being bought, the item can be dyed (via NPC or crafter, however), using crafting dyes / enamels / lacquers, BUT ONLY ONCE. Once the item is dyed, it cannot be redyed. Just a thought.