Kill a Favorite

To kill, or not to kill....
So you have this secondary character you really like, but the story dictates he/she has to die. What to do?
Ever run into this?
The first time it happened to me I thought I must be doing something wrong. After all, isn't the only indispensable character the protagonist? And who's story is this anyway? I'm the author, I decide who lives and dies, who's likable and who's not.
I've since learned it ain't so.
Sometimes a character is just that good. They are alive, real, impossible to ignore. I have to let them grow because anything else would be a lie.
So, back to the original question, live or let die? (Apologies to Paul M.)
I don't have the answer, except to say, "let the story dictate the outcome."
If the only way to get that satisfied feeling that the truth has been told is to kill a wonderful, likable character, then so be it.
On the other hand....