It is important to remember a mod issue though that happened with the old cap system. Which is most likely the reason why the bottom enemy presence bar was added in the first place.
The cap system in general got as an issue that basically you just need to get more people than the enemy inside the cap zone to capture. The easiest way would be to just get more people in and cap without firing a shot.
The enemy presence bar removed stealth from the game and I hated that. However as long as there is stealth people try to sneak people into the cap zone stay stealthy and do a surprise cap and move like to a single room where they cannot be found easily. An effect similar to the cap wagon tactic in tank maps. Aka people try to stay hidden in a corner or room of the cap zone on purpose and try to cap without the enemy finding them on time. I think the idea of the enemy presence bar forces attackers to come out and attack more, as the defenders know they are there anyway and would start looking already.
The willingness to hide as long as you are alive in the cap zone is in my opinion a fundamental flaw in the capping system and would like to see that resolved by an area focussed cap system. And see people focussing to obtain an actual overhand within any location. However I am against the removal of stealth as a means of doing this.
Having people hiding in the cap zone is in my opinion still loads better than immediately notifying that enemies are in the cap zone. So if the cap system were to stay the same I would still prefer the enemy presence bar to be removed.
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For the Icon on the overhead map showing that the enemy is capping my solution is rather simple. Only if a friendly soldier is in that same cap zone, should the status of that cap zone be shown in the hud on demand / overhead map.
If there is no friendly soldier in a cap zone then you simply won't get a status report on that cap zone. This should allow the enemy to sneak behind everybody's back and surprise cap.
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For those interested here are some discussions about cap systems in general, where capturing is based on the territory hold by players rather than amount of players within the cap zone. (A change in the cap system is my NR1. preferred addition to the roost arsenal of features).
http://forums.tripwireinteractive.com/showthread.php?t=34708
http://forums.tripwireinteractive.com/showthread.php?t=40735