Why would it make sense for a jumping puzzle in WvW to be a neutral zone or frankly any of the other suggestions you made? I too personally sometimes get frustrated when I get killed doing the WvW jumping puzzles, but is there anything wrong with them in my opinion? No.
You get siege blueprints for completing the puzzles, therefore stopping the enemy teams from being able to complete the puzzle has a tangible benefit. You are denying the enemy team from obtaining free siege equipment that they would then use to break down your gates. Granted you are right, some people are there with the sole purpose of trolling, but that doesn’t change anything. Much in the same way that you’re not going to take a keep by yourself, you can’t take an organized emplaced group by yourself. I’ve not seen a single place that you can’t get people out of with teamwork or even just a large number of bodies.
If there’s no one else there or no one seems to care enough to help you, then well I don’t know what to tell you except sorry, try again later. You couldn’t beat them, you don’t have a right to complete the jumping puzzle, just like you don’t have a right for them to let you into their keep so you can get the point of interest to complete your map exploration.