In Go (board game) under Chinese rulings how does the scoring of empty territory work?
It's already clear for you that a group with two eyes is alive.

By extension, a group that has enough room for two eyes is alive, even if the eyes are not formed.

At the end of the game, the human players would indicate - by a click for example - which stones are dead. The computer can then do the scoring.

If you expect the computer to figure out which stones are dead, then it needs to know how to play. There is now open source software that can do it, such as Leela Zero.