In the event you describe, blue deserves the win. Blue managed to reach the point and capture, and Red failed to remove them from the point for any length of time; while blue managed to constantly be blocking it.
I do find it interesting that you think Blue deserves the win. Surely blocking is far easier than destroying two ships at the same time?
That actually reminds me of when I played on Crazy King with someone. They flew their squid under the building surrounding the capture point to perma-block it while being immune to damage (couldn't get arcs on it). Cheap move, in my opinion, and very effective.
I think the issue is that Red does not get properly acknowledged for it's efforts in the score.
It certainly doesn't help the situation
In the event you described, this match would never ever end, as both teams are on the point at all times.
This is why I said it may need to be extended to allow capture via kills.
For example:
You kill an enemy ship who is on the point which they are capturing or have captured. It loses a chunk (goes towards neutral).
You are on the point which is neutral or you are capturing and kill an enemy ship. It adds a chunk to your ownership.
I believe (bearing in mind I haven't slept properly in the last week) that this would have the same effect as shortening the timer, but allow the team who is actually dominating the point to capture it through kills, instead of timer.
Thus my hypothetical match would go like this:
B captures the point via timer and starts accruing points.
R destroys B1, reduces the point to 66% B owned. B2 blocks timer capture.
B1 returns. B blocks timer capture.
R destroys B2, reduces the point to 33% B owned. B1 blocks timer capture.
B2 returns. B blocks timer capture.
R destroys B1, reduces the point to neutral.
Then every time B1 or B2 is destroyed thereafter, the point would become more owned by R (33%, 66%) until they had "kill captured" it and then R would start accruing points. Match ends 650-300 or something (depending how fast the kills were).
I think this would be a better reflection of capturing and doesn't cause other breakage. In fact.. this might make snipers more viable on CP as they can neutralise the point from a distance (but they would still need to be on the point to capture it). I'm not sure if snipers have issues on CP though.
Any slip on either side would play out as CP does now anyway e.g if B didn't get to the point in time, the timer would start and R would capture it that way. Each kill ends up with the timer being shorter, which is what you were suggesting.
Could this be a win-win(-win) solution?