Morrison intended Jean to have a bad death. The "bad" death was even referenced in Here Comes Tomorrow (by other characters.. I believe it was Ernst/Cassandra). I mean sometimes characters do not have big meaningful deaths look at Tasha Yar.
I loved Jean's long running subplot in Morrison's run and I did like her death scene in Planet X. I was excited on how she was used in Here Comes Tomorrow. Yes I wish her death didn't last as long as it did, but overall I loved Morrison's X-Men and I loved his Jean Grey story. In my opinion it was in a lot of ways better than Dark Phoenix Saga (because of how DPS was written - not all of Claremont's writing still stands up). Don't get my wrong, I love the DPS, but Morrison's run to me is the best X-Men run (by far).