stealth games always run into this issue. if you make it ultra realistic (ie if you're seen, they will go into alert mode basically indefinitely), it's too hard on the user.
i think of the way GZ and TPP do it as a gamey solution. a lot of people, myself included, in past games would just restart from checkpoints the moment you're seen. what's the best way to negate this problem? the player runs away and hides, waits. and then has to tackle the very same problem again.
basically, seen --> alert --> player runs and hides, waits --> everything resets. essentially the same result as restarting from a checkpoint. you still have to tackle the issue at hand
what you're suggesting might "appear" more realistic, but ultimately is still the same result: seen --> alert --> player runs and hides, uses cigar --> everything resets
is it really that important to change then?