I really only have two ideas - one, lengthen the amount of space behind the lie we are allowed to utilize. then we can still step putt behind our lie.
Or, define what a putt is not by how close to the basket you are, but by the motions and general positions used. I think we can all agree that there are certain mechanics involved that are present in everybody's putts to make them functionally distinct from drives and approaches, and I can't fathom how someone could try to gain an advantage by changing how they fundamentally putt to skirt the rules.
Then, if one chooses to use this style of throw, one must not allow their feet/supporting points/whatever to travel beyond their lie. Basically, stay behind your damn disc until the disc hits the ground.
I think it would be hard to draw up, but defining a putt based on distance or area makes no sense when you don't actually have greens.