there are several approaches to penalize someone capping. The capturing radius is really not that big, you can just surround it by red cover if you want to make it harder for specific points. But in general, it makes the game faster paced, if you don't have to dedicated a squad to capping. Makes it harder to camp a point. I found it to be a good change from what i have experienced.
As i said, this maybe a doctrinal ability, but not from the start.
If you look at vcoh, there are infantry squads who can cap faster. This creates diversity in gameplay and is linked to the wehr vs. USA gameplay by wehr being defensive in the beginning and getting more offenive in mid and late by having infantry avaiable, which also can cap faster.
As i understand your post, you want every infantry to cap at the same speed, being able to fight normally while capping, but penalize this by red cover.
However red cover is a different gameplay element than capping speed and taking more damage while using special abilitys. You can have this red cover around VP´s already in coh1 (which will be the same then in coh2), but removing the current capping mechanics will not improve the gameplay, but make it more poor, because Capping will be penalized always in the same way: red cover.
This will make the game more fast paced, but also more simple and boring.
Seriously, there is no need to remove things, which have been proven to work just fine. What coh2 just needs to do is to improve the multiplayer support like the replay system. Look at Starcraft 2, how versatile replays are there.