Of course, you are right. Energy drain in any form is lethal to low level characters, but my other point is still valid.
It makes Good Fort save characters almost immune to energy drain at high levels and makes it more deadly to weak Fort save characters. The existing negative level mechanic didn't discriminate as much and was more equally damaging to all, except regarding removing of the negative level after 24 hours.
Don't get me wrong, I still love your idea. I'm just thinking out loud to consider if it could be modified to make it even better.
I think variant ideas and new concepts like this are great. Innovation is rarely a bad thing.