If you kill the Cats, the CAG and the Captain are thinking something happend, but they have bo proof. Later you will have to help the Cats again, and when you land the Captain and the CAG will be pised. If you don't decide to save them the second time you will be cort martialed.
Starfury- It helps if you say which mission you have problems with, anyway I think I know which one you mean. You have to open you're nav map and select the 2nd nav point by right clicking on it with your mouse. You may have to do it couple of times. Than you have to auto to the 2nd nav and help the pilots there.
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A good soldier is not the one who die for his country, it's the one who makes his enemy die for his.
Gen. Patton