I have realized that when fic writers (myself included) want to undo/erase/change something that has happened in the canon (often a romantic relationship that interferes with our ship or one of the characters’ death), there are three basic approaches to take.
1) Either ignore the problematic canon all together or get rid of it approximately one sentence (“Gee it is a good thing you were wearing a parachute when you got pushed of that cliff”, “After Character X and I decided to call it quits…”).
2) Take some time to explain the change (because you feel guilty) but do so in the most convenient way possible (this is usually where all the fucked up character assassination happens); because, really you just want to focus on your OTP (Character A goes crying to Character B when their canon partner is awful).
3) Use the obstacle as a centerpiece to your story and why it is happening now and in this way. (Thinking the other person was dead forced the remaining half of your pairing to confront their feelings and not waste any more time. The realistic reasonable relationship struggles that paired off ship half is having with their canon partner makes them reconsider what they really want in a relationship.)
The most important thing I have realized though, is that I am actually fine with either option 1 or 3. Sometimes we feel like the canon made a mistake or just aren’t willing to give up on our pairing and we aren’t interested in justifying it. On the other hand, working your way through canon event obstacles can be very compelling (if handled in a not terrible manner). It is usually option 2 where we get all kinds of gross problems; because, we treat characters as obstacles to our ship instead of people… we make them the villain for the simple fault of being in the way.
This isn’t surprising, considering that as a society we do this all the time. How often do people badmouth someone who is “with” the object of their affections? I know I used to. How often do we bitch about someone who got a promotion we wanted? It is fine to still want what you want, but we have a sociological problem with vilifying those we envy.