Wiring it in like this is suboptimal because this way you might never see the LED light up if a still photo is surreptitiously captured. This has been a problem before: illicit captures that happen so quickly the LED never has time to warm up.
Controlling the LED programmatically from isolated hardware like this is better, because then you can light up the LED for long enough to make it clear to the user something actually happened. Which is what Apple does -- three seconds.
I don't see why they should be mutually exclusive
The only time that isolated hardware approach is benefitial in terms of costs would be when you already have to have that microcontroller there for different reasons and the cost difference we are talking about is in the order of a few cents max.