Uh....really? I over-pronate, but have never found any hiking boots that made the condition any worse. In fact, they almost always help, as the firmer soles and shanks neutralize foot-roll. (As an aside, I'm sure everyone knows this, but pronation is the process of your foot "rolling" inward after the heel strikes. Everyone pronates—or should—but if the roll exceeds 15 degrees, that's called over-pronation and can be a problem.)
Also, running shoes are not "neutral," nor do they necessarily correct for pronation, unless you are wearing stability or anti-pronation shoes. If you aren't, then I think what you are feeling in hiking footwear is not more pronation, but an absence of it. I see people who over-pronate so badly they look as if they are running on the inside of the ankles. Yet to them it feels normal.
So I'm not sure I have any good advice. My current favorite boots are the Scarpa Kailash GTX ($199). I've found them to be very comfortable and super-stable, yet lightweight. I must have 200 miles on my current pair without any problems. In the past two years I also have worn boots from Garmont (Zenith, $160), Asolo (Fugitive GTX, $215), Vasque (Breeze GTX, $160), Oboz (Sawtooth Mids, $135), and Merrell (Moab mid, $125), and had good success with all, from a fit and stability standpoint.
I do like after-market insole inserts such as Superfeet, but at $35 they aren't real high-priced. I think they add some stability and improve overall fit and support.
I recommend you go to the Seattle REI store on a quiet weekday morning, ask for their best shoe-fitter, and see what you come up with.