You actually can heal your essence. It takes a long time and costs a lot of money to do so. Check out Chrome Flesh: Genetic Restoration: Revitalization.
Also, if you replace all of your limbs with cloned limbs, then it doesn't cost much (if any) essence. Culture Bioware replacement limbs cost no essence. The trick is trying implant a cyberware limb, then re-replace it with a cloned limb. At that point "the damage is done" and like it has been said, the road to recovery from that point is long.
For most people, though, repairing that essence loss isn't really going to affect them. A lot of people are totally going to go the whole "what did my soul ever do for me?" route and just not care. For magical people, losing the essence in the first place is what loses you the magic, healing it back isn't going to get it back.