I converted a car from disc/drum to disc/disc and I put a Wilwood proportioning valve on it in place of the factory thing and never had a problem. It was nice to be able to adjust the bias front to rear.
All the the manual prop valves do is reduce the pressure that is sent through them. If you put a manual prop valve in you simply limit the pressure to the rear brakes so that they will lock up earlier or later. You want the rears to lock before the fronts, but not much.
If you remove the factory valve you will lose some safety features such as the brake warning lamp that activates if you were to break a line or something. This may be ok for you, but doesn't really up the resale value.
I don't know too much about jeeps, but I know it takes more pressure to actuate drum brakes than discs. The drum brakes have to over come the return spring pressure before they start to work, while the front calipers require very little pressure before they start moving. Many manufacturers put some sort of valve in there so the front and rear brakes would actuate at the same time and not wear front brakes prematurely. This may be part of the master cylinder or part of the valve you want to remove--not sure on the jeeps. Just some things to think about.