[Q]

Saxon for your first question:
No, I think it is better to keep the old low level counter intel and put it at the end of your intel project list (highest project number). The attacking enemy projects will first deplete the counter intel project at the end of the list. Once it is depleted then you can cancel it. Deactivate the option "divide points equally" and all your available intel points will go to the first project and there you put the new high level conter intel. Just make sure that it is not completed within the next turn or you will loose your points!
Your second question: That's exactely my opinion too and therefore I changed it now in my ongoing game. The effect is enormous: My attacking intel projects have now a realistic chance to succeed, but I also have to spend much more of my intel points to defend myself against the attacking projects of my enemies.