The Joker killing Rachel would be perfect for a couple of reasons.
One, even though Batman already views Joker as a homicidal maniac and is intent on taking him down, Joker killing Rachel would be a good analogue to the comics and him killing Robin. Joker sees that Batman is indeed close to someone and he wants to hurt Batman in any way he can, so he goes after Rachel, just like he went after Robin in the comics.
Two, with Rachel killed, they have the perfect time to introduce Harvey Dent as a hot-shot DA. He's good-looking, charming, smart, but he also has an ego and after hearing about this Batman-character in Gotham taking down criminals, is a bit offended and decides to clean up Gotham himself from inside the system. He's ambitious but also naive, so he does not want to make an alliance with Gordon and Batman at first, but after building up a perfect case against some mob-family in Gotham and getting it thrown out of court, understands that the law isn't infallible and he has to do whatever it takes to take the family down. So, Gordon, Batman & Dent start working together, get enough evidence and a good judge to take the family to court again.. and then comes the acid. Enter, Two-Face. Or, we can have him take the Joker to court and have him throw the acid. Either way, we get Two-Face. And there's always the possibility Batman, Gordon and Dent are working to bring down Penguin's arms-cartel (or is that just a rumor?) and one of Penguin's henchmen bathes Harvey in acid during a trial.
Three, we have a good explanation why Bruce's love-interest is gone, instead of going the route the old movies did and just make the women disappear. With Rachel gone, we can leave a door open for Ra's Al Ghul's daughter to appear in the third movie to continue her father's work, but at the same time, have her fall in love with Batman and explain that to be with her, he has to become the new leader of the League Of Shadows. However, Bruce can't allow that so it's a good "forbidden love" type story.
