I'm the opposite.
I hated that about the 89' Batman because it made absolutely no sense and was completely unnecessary IMO. It also wasn't true to Batman's origin in the comics, which is the source material being used for ALL of these films. The Joker is supposed to be obsessed with Batman. Not the other way around. The Joker enjoys (albeit in a sick and twisted way) ANY type of contact he has with Batman. It's always The Joker doing stuff to attract Batman.. so The Joker can have contact. That's what he enjoys.
That sick relationship completely dies if The Joker murdered Batman's parents. Because then, just like in the 89' film Batman would be the one obsessed. Batman would be the one constantly trying to make contact with The Joker, etc.
Also (in the comics and even in the 89' film) Batman made The Joker (Red Hood storyline) so that sets up the connection between the two. But it's a connection that The Joker is fixated with. Not Batman. Since for the most part Batman isn't even aware that the Red Hood was Joker (at least initially).
And in TDK, the connection is how much fun Joker has 'playing' with Batman. It's an adversarial relationship. The Joker becomes obsessed with Batman because to him, Batman is the only worthy opponent he can find (since he pretty much has his way with everyone else in Gotham).
IMO both those elements work in both films without The Joker murdering Batman's parents. Seriously.. to this day I still think that element of the 89' film is stupid.