Well, sure, you can run in hiking bootswhat do you think they do in the Marine Corps? But are you sure you want to? Run, that is. From your self-description you sound like a knee or foot problem waiting to happen. Why not just keep hiking? Its great aerobic exercise, easier on your joints than running, and you already have footwear you like.
But, assuming you really want to do some running, Id pursue two courses of action. One is to see a podiatrist and find out if there is an orthotic or some other device you can insert into your shoe to improve foot stability. Its possible that an off-the-shelf product such as Superfeet ($40; superfeet.com) can also be used to give your feet more resistance to pronation.
Then, you might try some trail runners. These typically have heavier midsoles than traditional running shoes, and a little heftier uppers as well. So youll have more foot protection, and they may better resist pronation. Salomons XA Pro 3D ($125; salomonsports.com), for instance, have an EVA midsole of varying density and a nylon flex plate for more foot control. Montrails Hurricane Ridge XCR ($125; montrail.com) has a medial posta high-density piece of material that counteracts a pronators tendency to roll his or her footas well as all-around high-end running features. Asolos Tenacity ($99; asolo.com) also has an EVA midsole with two density levels and torsion-control plates. Lastly, New Balances 810 trail runners ($85; newbalance.com) have good shock absorption and motion control, plus come in widths for better fit.
Id also suggest you go to a full-service running store and have someone fit you carefully.