Honestly, that seems like splitting hairs to me. You still have the implants and you're still using 1 full point of Essence (you just get extra Essence from the Quality). I'd say you should still lose the appropriate amount of Magic.
You're not gaining a point of essence, rather you're not incurring any essence cost for the point of bioware. There is an important distinction there.
With the rules as written, your first point of bioware (taken at character creation is what I believe the intent is, going by the full text) does not cost any essence. In other words, when calculating magic/resonance you are subtracting 0, so you don't lose any.
This is very different than *gaining* a point of essence, in which case what you say would be how it works. But, thats not how the quality is written (and the quality would be almost worthless if it worked this way).