Allied ground attack aircraft (jabos) were the bane of German infantry late in the war, so one side sometimes dominating the battlefield with aircraft in the game is not some unrealistic flaw or glitch that is being taken advantage of. Whether any anti pilot stacking measures are taken or not, like Anger said, ADAPT. Learn the habits of the pilots in question as to where they like to strike (it's not always the base) and what they like to keep on the lookout for and then try to minimize your deaths from them (different routes, better use of cover, spawn at a different flag, try to sneak out of the base and grab a flag, etc). They all have their individual "signatures."
By this logic..."team killing"...aka friendly fire....should not be punished so harshly. It happened. There was one campaign over africa where an air attack was devastatingly fired upon by AA allied friendlies, resulting in much death and destruction. It was an accident...unintentional.
Now, if you see someone intentionally or habitually doing it...that is much different. Like to try to get equipment and such?