The ability to resurrect Nei would reduce or negate the impact of losing her.
Perhaps adding a side quest to gain a mute, emotionless Neifirst or something along those lines, would allow the player to keep a palette-swapped Nei sort of NPC in the party while maintaining the loss that the main character endures by losing her.
Well, unless there was some SERIOUS editing done to the game, Nei would have no lines or anything like that after Climatrol, since the game would still think she was dead. So, she would be mute and emotionless, and would have no part in the ending, etc. She'd just still be a playable character.
EDIT: Once again, making a sidequest would require some serious changes to the game's code. What I think the OP was talking about would be just a simple change where the game recognizes her as still being either mandatory or optional rather than unselectable when you go to your house to reorganize your party. There's a Game Genie code, as was mentioned in this thread, to do it...but there must be some way to actually edit the game so that it doesn't change her selectability (for lack of a better word) after Climatrol. Unless someone edited further, she'd have no lines or would not be part of the storyline in any way. The storyline would go on as it normally would have without Nei.
FURTHER EDIT: Has anyone used the code mentioned in this thread? If so, I have a couple questions about it:
A) Do you have to turn on the code every time you want to change your party, or does Nei stay in your party for the rest of the game after using it once?
B) If Nei dies after using the code, can you revive her at the clone lab as normal, or do you get the "it doesn't really work like that" message like you do after Climatrol, necessitating further use of the code?
FURTHER EDIT AGAIN: Even if the game were altered so that Nei had an actual part in the storyline after Climatrol, would it really lessen the impact of losing her? It's EXTREMELY unlikely that anyone except a veteran of PSII and PS in general would be seeking out this hack. Thus, anyone who would play it would know exactly what the impact of losing her was. It'd just be replaying the game from a different angle.