The people in the Scenario League will probably have a better idea of the applications that are out there.
I doubt very much that there is an application that will allow you to remove rivers, because these kinds of applications are usually built by scenario makers, and a scenario maker that didn't want rivers would simply not make a map including them.
If you don't mind knowing the map ahead of time, you can generate it in the Map Editor, and manually remove all the rivers before saving the game.