So the question becomes whether cybernetics make magic more tiring or more difficult when casting spells. If it becomes more tiring since you have less "essence" then strain costs should increase.
If it is more difficult then it could be a combination of setback dice and difficulty increases or automatic threat (or even failures) that are gained as casters get more implants. Each .5 Brawn (or fraction), add one threat to the casting check. The only problem with this is that casters with a high Brawn can have more implants before loosing their ability to cast and will accumulate more potential threat.
Alternately you could do a combination of the the above options.
As a side note, in Shadowrun, characters can take enough physical damage to reduce their essence. This should be added to the Crit Table somewhere above 120 (I dont have the book in front of me).