My lw tried on many pairs of dance shoes and only found one pair that comfortably accomodated her high arch (without digging into the tops of her feet). The lowest heel in which that model shoe is available is the 2.5 inch heel she bought.
Number one is probably the support for the arch, as your wife already figured out by herself. I wish someone would have given me that advice. Number two is almost certainly to get metatarsal pads, they make a lot of difference for many women (see, if the arch is high and it tends to be unsupported the pressure on the front part of the arch tends to get high, which in the long run can damage the feet. The metatarsal pad supports the front part of the foot which otherwise is under too much pressure). Number three, listen to all the things Gracie have said - my guess is she, your wife, and me have similar feet. It is not that uncommon, and this kind of feet are sensitive to certain kinds of stresses.
Number four. If your wifes heels will make daily antiinflammatories necessary, like for Gracie - do you really want her to wear them? I do not understand why women are supposed to be happy for waking up without pain in the feet. I would expect that to be normal...
I hope I am wrong about your wife's feet. Probably a check that she does not have the kind of feet that I have would be worth it. I paid like 35 dollars/25 Euros to have my feet investigated and I am sure it is worth it to have it done. If the outcome is "you need not worry", then that is great.