Scans_Daily

The commentary track on that movie actually goes into some detail about that. This was to be the last continuity appearance of Harley as a character, so they knew they could do things with the character that they couldn't/wouldn't before. They could make her actually evil and not have to worry about what that would do to her "rep" long term.

Even allowing what she did to Tim was hideous, Paul Dini desperately wanted to keep her alive (since he viewed her creation as being one of his biggest contributions to the Batman mythos), but Bruce Timm and everyone else involved viewed her involvement in the scheme as being fundamentally unforgiveable (Far more cruel than anything else we'd seen her do directly) and felt she had to be killed off.

This is why she DOES die at the end of the flashback, adding her in at the end of the movie was Dini making his displeasure manifest, and it was left in because it added a moment of comic relief.