The way aquifer tiles work is that they do not 'appear' until they have been 'uncovered'. Now, in older versions that meant that you either had to dig into an aquifer tile, but if 'something of note' existed below the aquifer, that embark tiles worth of aquifer would be uncovered immediately upon embark. When you remove the aquifer tag, all uncovered aquifer tiles lose their aquifer tag, but any that had been uncovered are permanently aquifers regardless of changes. The same works in reverse, any exposed non-aquifer tiles of any specific material, if changed to have the aquifer tag, will not become aquifers, but any of those tiles that have not been uncovered would. Too bad that this is all moot in 2010, but it helps get an understanding of what is going on here.
Now, in DF2010, every embark tile has something of note under it, so the entirety of your map is 'uncovered' (not the same as exposed, it is more a case of the engine actively tracking the tiles), that means that if you had aquifers enabled when you initially embarked, all layers that had the aquifer tag will retain that tag. What this also means is that if you do not embark on the area until you make your changes, they will take effect, whether adding or removing the tags. The only reason that it would seem you need to regen is because of the mechanic I outlined above. I hope this makes some amount of sense, if not just say and I will try to explain better.
But in short, you can generate a world with everything normal, then go into the saves raws and fiddle with your aquifer tags like in your OP, use the finder to find a site, then without embarking(cancel out of the embark process), go back and change the raws to where they were, then go back and embark on that spot you found.