I don't have any experience with glass jons but I do have considerable experience with aluminum jons in windy/rough water.
Unless your shoals absolutely demand a jet to navigate them I'd go prop, and get really good with your tilt/trim and water reading skills.
Having that lower unit acting as a keel on your drifts back downstream will help alot in a stiff wind.
You'll eat up a prop or two in the beginning but you can learn to run a hell of a lot shallower with a prop outboard than you might think without tearing anything up. Plus, your clients will be alot more at ease watching you finesse the rig through a skinny spot than they will while white-knuckling a shallow rock garden or sliding around a narrow bend Tokyo Drift style..
Everyone seems to think that if they can see the bottom then they need a jet pump, and that's just not true at all. Give me 14" of water over a shoal and I'm good
My hangups with a jet pump are.....
1. Lousy control at slow speeds.
2. They can't hold the water in waves.
3. Jet rigged boats are flakey about load distribution.
4. Lousy control at slow speeds! (Yeah I said that twice)
If navigating your stretch of river calls for crossing numerous ankle deep shoals and you have a major problem hopping out in water shallower than your knees and doing a little hike-a-boat then ya gotta have a jet, but I run."jet boat water" in prop rigged jons quite a bit and I haven't busted a gearcase or completely destroyed a prop in years.