Hm, but the commander sees all the markers, right? Maybe it's worth looking into the code that makes that possible, if it's not buried too deep.
Or you could add this to the commander, seeing as PR has devised a way of placing multiple markers, he could be allowed to place a single numbered marker to denote what each squad is doing at the moment.
He could even try to "confuse" the other SLs into thinking that another squad is attacking the flag instead, diverting them from an unimportant one, although I'm not sure if that's a feature or a serious flaw (although it would nicely simulate the problems of WWII chain of command where the orders were often completely messed up, and the real situation completely different from what was shown on the HQ's table
)
Overall, if it could be implemented, great, otherwise I still think that giving the Commander the power to place permanent markers for spotted stuff is the way to go. It would surely up the communication aspect if the commander could play his own "find out where the enemy is now" metagame. With decent admins and a cooldown time, even trolling commanders wouldn't be such a problem.