This sort of happened with Stargate Universe IMO even though they didn't necessarily assassinate the characters of the previous shows, unless you count the tone of the show as a character (and I'd argue that it sort of is). The fan groups didn't really overlap, and they lost more than they gained.
If I recall and also according to what was said at the time, I think that was more a network/MGM decision than the decision of the team(s) that ran the
Stargate shows.
After the eighth season of
Stargate: SG-1, they wanted to end the show and start a new one,
Stargate Command, which would have the same setting but with the new characters and villains that were introduced in the ninth season. Doing so would also have lowered production costs as it would have been considered a new show and not have the automatic increases associated with a long running show. And that would probably have been beneficial to MGM which was in some financial difficulties. But the story is that the SciFi Channel wanted to be able to claim to have the longest running scifi franchise so renewed SG-1 for seasons 9 and 10. Then, you know, cancelled it after they got their ten years.
And, you know, announcing the cancellation right after the 200th episode, yeah, bad idea.
So, anyway, first mistake, maybe? Then they tried to appease SG-1 fans by shoehorning Samantha Carter into
Stargate: Atlantis which probably ticked off both fan groups. That only lasted one season before they replaced Carter with Woolsey, which, IMHO, worked better as a replacement for Weir than Carter did. I mean, having Carter there just felt like they were doing it to appease fans and not because she was a natural fit. Dr. Jackson would have made more sense, you know?
Anyway, so then they cancelled
Stargate: Atlantis in favor of
Stargate: Universe and, you know, at that point, I think they pretty much ticked off a lot of the previous fanbases. The tone was different and General O'Neill and Daniel Jackson didn't seem like the same characters in their occasional appearances.
And I think a lot of that was the networks not the showrunners because they had successfully introduced new characters before without smearing over the old ones.
But who knows what might have been. Possibly,
Stargate Command and
Stargate: Atlantis could have run concurrently for a few more seasons and maybe they could have introduced
Stargate: Universe while one or both of the others were still running and not had as drastic a change in tone and who knows?
Of course, MGM's financial problems loomed over everything and basically led to the whole franchise kind of fizzling out. And now Amazon owns it, so we'll probably get something like the young hipster SG-1 team they mocked in the 200th episode.