Warning: Wall of quotes ahead.
The only issue I have with the OP suggestion is that it would turn the capture point maps more into DM's. It would just promote even more combat around the control points, making your ability to destroy your enemies the largest factor contributing to success. Rather than using coordination and tactics to outmaneuver your enemies to gain control of the point.
My thought is that the penalty would be large enough where killing ships is encouraged, but not so large where it becomes the overriding factor. Plus the killing of ships isn't going to directly affect your score unless you already hold the point (at 100% full). I was thinking around 10 seconds worth of "uncontested" per kill.
If kills helped push the capture meter or score, teams would just clump up and rush each point together. Essentially returning to DM tactics of 'kill the enemy to win'.
If you only have 2 ships going directly to the point and the other 1-2 going to the next point or running interference, you're still limited to losing those 2 ships and that 10-20 points or so. Furthermore, if the enemy team decides to 4v2 you on the point to secure those kills and essentially farm points that way, you're easily going to secure the next point with your other 2 ships -- a far greater point advantage overall. So there is still incentive to split your forces, especially against anyone who doesn't.
Limiting the affect only to the region near the active point means that there is still no penalty for running interference, even if you're killed in the process.
I think the only way to keep the essence of a control point map while fixing the problem is to always ensure that deaths are not advantageous. If you know your enemy won't spawn next to the point, you can feel safe to destroy them, instead of just maiming them; and you're less likely to feel the desire to end your own ship, or let the enemy finish you. There's an number of ways to do this, such as changing the spawn locations depending on which point is active (and how much time is left on it). As ships tend to head to the next point well before the current point stops being active.
Changing spawn locations and my original suggestion aren't mutually exclusive, and in fact can complement each other nicely. One perk of my idea though is it's theoretically easier to implement and balance overall, as it can be one sweeping mechanics change rather than having to examine each spawn point and potentially having to add and balance more of them.
Here are a few radical ideas...
1. Have a dead period when the match starts. No point is active, and no indication is given as to what the next point will be. After 60 seconds or something, the first point will activate. This prevents one team from having an advantage on spawn, and encourages both teams to head towards the center of the map to fight over who will have the shortest possible route to all available points. The alternative would be to make the center point always active first, so no team gets an advantage.
+1 to the dead period idea. It might not encourage teams to head to the center though -- making a gamble on 2-4 of the 5 points by sending a ship to each is also a possibility. (This isn't a Bad Thing(tm), though.)
2. Stop the points from being in alphabetical order. Whoever owns a point when the timer ends (both teams if no team controls the point on timer end) gets a pop-up telling them which point is next. 30 seconds later the other team is informed of the next point and it is displayed on the map like normal. This means you will want to fight to the last moment to control a point. This stops the current system of completely abandoning a point if there is less than 100 seconds left to it. As the controlling team, you can't leave point and risk not knowing where to go. As a capturing team, you want to try to get in and and take that advantage away from your enemy so you can get to the next point first. The notified team can then split up and send decoys to other points to try to lure the enemy away from the actual next point while they don't know where it is going to be.
I'm generally not in favor of amplifying any advantage the currently winning team might already have, and this would do precisely that. I also feel that accepting a minor defeat to try for a victory elsewhere should remain a valid strategy, and this hinders the "try for victory elsewhere" approach.
Due to the current nature of CP, there's always a time where a point is a lost cause simply because there's no way to turn it back before the countdown expires/enemy team wins, even if it was completely uncontested the entire duration.
3. Make the point timer only active when a team controls the point. The full amount of points must be collected by the 2 teams combined. There will be no points where neither team collects any resources before the point moves on. This will help reduce the amount of time some crazy king maps are currently taking.
I actually liked the 90 minute Crazy King game we did for Iron Fork last week, but I agree that most people don't expect games to take nearly that long. That said, I don't think this would work with the current timer durations (you wouldn't even visit all 5 points on the map in a match) -- but it could if they were reduced.
The flipside is that battles in the form of "Just don't let them cap" are pretty exciting, at least for me.
4. Bring back resource race!!
Before my time, so no opinions here