Every time there's an Edition change in Forgotten Realms, they take the pruning shears to the various established characters and the deities. Some get awesome deaths. Azuth the god of mages, an ascended mortal that got his position by kicking the ass of the previous god of mages, pretty much gets eaten by Asmodeus to fuel his ascension to godhood.
For the 4th Edition, they literally drop a continent on several Realms to get rid of them.
Rumour has it that Mystra, greater deity of magic and A God Am ICanon Sue, got killed by getting hit on the back of the head, along with numerous other Canon Sue characters, though most of them departed in ways that imply they can be brought back *groan* .
In addition to the actual deaths, the 4th Edition also wrote out a fair number of gods (some very old and quite prominent) by retconniningly revealing that they were actually aspects of other gods all along. The gods may not be dead as such, but they were definitely written out of the setting in an unexpectedly anti-climactic and mundane way...
The Squats of Warhammer 40,000 got a hive-fleet dropped on them. Some fans argue that the Squats are Old Shame and deserved to be removed, while Squats fans will invoke They Changed It, Now It Sucks. Games Workshop has stated numerous times that they have no desire to revisit the issue or argue about it with fans, however they did include a reference to the Squats in the latest version of the game listing them as a non-extinct species, and they still allow them to be played in official events as long as the figurines are drafted under an officially supported army's codex.