I think he mentions his memories were transfered into "program data", so I guess his brain is robotical too
Initially his brain isn't mechanical, but by turning his memories into program data which his human brain is connected to, they ensure that even with his human brain dying, he would never forget.
As for immortality and punishment. Such a thing as imprisonment and the death penalty are pointless to the old man Dr. Weil who's already at the end of his human life. Because of his age, death is simply the easy way out for him.
Giving him immortality isn't about making him experience eternal life. It's about making him experience endless suffering. He has a human body that's constantly dying and reviving, thrown into a world without light and nature. He is simply driven insane with endless agony by that pain. Add to that him being far removed from civilized life and his armor lacking any of the capabilities it has now. He'd have to literally crawl back to Neo Arcadia, to his old lab, to get himself back into reasonable shape and stop the endless pain.
Keep in mind though, Weil's state of being at the end of Elf Wars is one not really known, but the above is the conclusion I came up with when brainstorming about the details of Elf Wars.
It's probably the same day where you say "I have no [tornado fang]ing idea how to put tits on that, Zan. Your question has left me stumped"
I'm probably shooting myself in the foot here, but Sub Tank probably can't put tits on tits. Which sooner or later I'll be stumped by sub tank's question.... unless he actually succeeds.