Beckett's role ended realistically when she became Captain, there's no realistic scenario where she goes out on all those cases, so they're already sacrificing a truckload of credibility this way, if she would/should've stayed, she should have stayed suspended and join Castle Investigations, that would've given a long-arc to develop, and it would've given a chance to move away from all the conspiracy nonsense.
I love conspiracy shows, but Castle's 5 consecutive Conspiracies(because it's like crack to the writers apparently, they can't stop stacking 1 ontop of the other) have all been flimsy, and broke the characters, fierce, relentless Kate(from the early seasons) became a wishy-washy, passive little victim, completely accepting the dominance of the people that murdered her Mom.
From a Character perspective, Kate would've killed 'em all(in the first seasons).
The same with Castle, Castle's character is an adventurous, boyish dreamer, but he stepped up when Alexis was taken to France, and he learned his father was a CIA agent, which should have matured, and created a more focused, and driven character, but again, a new conspiracy comes up, and it's wishy-washy cowardice all-round.
Lanie was already on/off with Pearlmutter so it's sad to see her go, I like Tamala on-screen, but it's not a major shake-up.
Beckett though, effectively ended her run on Castle when she became Captain, there's no way around that, and if she can take out the conspiracy-angles it would be a great reset for the show, to get back to it's strength, quick, light-hearted adventures, because the writers are completely lost in their own conspiracies at this moment.