Usually it's easier to get the government in line than to prevent some technology to be developed...
This is simply the same trend as ATMs replacing (some) bank tellers many years ago.
Will it be easier to perform and abuse mass surveillance? Sure. Will people with something important to hide still wear disguises? I'd bet yes.
My stance is that we can't fight progress, but we can start fighting the people bent on abusing the powers that progress bring. Identifying them is another issue (perhaps some form of facial recognition? :)
Facial recognition systems can be (and are) trained to not be fooled by things like facial hair, hair changing, eyeglasses and sunglasses, hats, etc. Although it can obscure your features for sure.
If someone does something really odd to try to avoid the facial recognition (I've people posting things like making your hair non-symmetrical, or just avoiding the camera in the first place) then they just train on those things too. And that person gets flagged as being really suspicious. And things like full face masks are banned in some places already.
This will have two effects.
People who are truly suspicious for nefarious reasons will gradually stop being so.
On the other hand, many will be incorrectly flagged as suspicious and harassed without reason.
The trick is to strike a fair balance between the two. But who decides what's fair?
Automated facial recognition is a serious privacy concern, it's not just about the slimy despicable thing facebook is. For example, in the uk where there are more cctv video feed than people to watch them, an automated facial recognition can track you around constantly. Their current automatic number plate recognition is already a serious privacy concern.
Remember 7th cube's voyeur's dream[1] released in 2005? the same but with more camera now being able to identify you based on your facial features. [1]: http://www.pouet.net/prod.php?which=16410