This is it. The most controversial episode of Spider-Man: TAS. Personally I enjoyed this episode. Part of Spider-Man's character is he can never be truly happy. They couldn't kill anyone in a "kids show" so they killed off a clone. Not a bad compromise. Christopher Daniel Barnes is at his finest here. He does an incredible job conveying the emotion of the scene.
I also understand why many others are critical of it and/or think it ruined the series. You do feel kind of betrayed, learning that MJ is just a clone. It makes you view the previous episodes in a different light. However, even though she is just a clone, I believe she still acted and behaved the way the real MJ would (since she had all her memories and emotions).