Yes, but originally she runs away, even based on the event of the maps, she is not with you even during Nali Village for most part, she was usually ahead of you, you see her running etc. That was explained in the scenario as well and as well as in the map events, there are some unused specialevents around which hint for that even.
If she was planned as a side kick it was really during very short part of the game, even in those levels it would be minority. But I don't think it is worth it personally, I wouldn't know what dialogue to choose, without more proper design doc, for each designer there was detailed scenario doc explaining events in his own maps and we got these missing.
I can make a scene with her running away and disappearing, that's easy to do, or even make her as sidekick in one map, but I would still advise against the sidekick thing, she would need to not die, so it would be something like Chryss in the end of ONP, with her you die too or game ends, but it wouldn't be good for coop either way, I think it is better to leave the sidekick idea altogether. In daikatana coop the sidekicks were removed due to this reason. The N64 version didn't have them as well, only in cutscenes and scripted sequences.
In ONP last map, the trigger which makes game end is disabled for coop, I could make it same, but there is a problem, she would die in coop and what, next map she would be there in some cutscene, not good really.