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That's true, she basically just disappears for the rest of the game on PS1 neutral. So, there was no reason they couldn't throw her in there. Actually it's kinda the same in the law route, if you don't kill her she basically just disappears after chapter 2. Probably why she can join in both the law and neutral routes on the PSP version, it was kinda left unresolved either way.
You know if they took the extra story bits and content from the PSP version, and made the gameplay something in between both versions (i.e. skills but no weird leveling or loot system), it'd probably be the best game ever.