@Adzling
I disagree that they are the equivalent of full body armor. Full body armor is visible and intimidating to everyone. Non-visible magic is not, and will not disturb the vast majority of the population. If someone walked into a restaurant today in full body armor, most normal people would grow concerned or panic. If they walked in with an invisible power with no discernible effect, most people would carry on oblivious.
Those spells are more in line with attribute enhancing ware (as you mentioned), which to me just having them activate shouldn't cause concern without coupling activity to cause concern. When investigated, passing a SIN/license check should also easily dismiss the issue, again without coupling activity.
@Hobbes
First, the FAQ says Combat magic higher than Force 3 (not all magic - specifically combat, and mental manipulation of any Force).
Your point of not knowing specifically what spells are what is fair, but other than a scant few mental manipulation spells, how many negative spells are there that could be afflicting/Quickened on someone without obvious physical signs? The answer is very few.
The player should never be trying to "pull one over" on the GM. Likewise, the GM should never be trying to penalize a player simply because they don't like a valid game option the player used for their character. This isn't a competition between the player(s) and the GM. It's about fun. If the player has fun with the Quickening option for this character, that's acceptable. If the GM wants to monitor the character closely and respond to suspicious activity or blatant spell use the FAQ calls out as always getting a response, that's acceptable. Use common sense, the FAQ, and basic courtesy and things should be fine.
Quickening is a strong option, but it is hardly the only strong option - especially in Chicago where there was a near constant background count. It doesn't need a ban any more than ware does.