Just a historical note, this actually isn't as uncommon as you might expect in the modern presidency.
Obviously Trump surrounded himself with far worse people than his predecessors, and he's churning through them at a pretty epic rate in some cases, but every single one since Eisenhower has faced a similar semi-faux "crisis" where they had to clean house and reorganize things within their first two years. It's a factor of our modern system where we don't have patronage officially anymore, but we obviously do and campaign staffers don't transition well into administrative positions. Just to use the Taibbi piece, Bannon basically pulled Trump's campaign out of its tailspin but he never had the skill base to be a staffer, neither did Priebus really. Karl Rove didn't, and it wasn't until the second term when he tried to actually take this kind of power and fell flat on his face. We can be overly nice to Trump and say he's realized this and so he's dumped out all these people in favor of General Kelly and so on, which also fits with his long known fealty to military members. Trump never really wanted the GOPers he fought against for two years, but accepted a bunch of them on the assumption they would be assets in dealing with Congress, then he realized they aren't, has flailed a bit turning to people he trusted like Kushner or liked on TV like The Mooch, and now with North Korea and all his plans failing in Congress and so on he's maybe had a "okay, maybe we'll get a bit more serious about this" moment. He might even see Bannon as more of an asset outside the White House, I mean the guy essentially disappeared for months, but now he's free to reorganize Breitbart and the like into helping Trump pressure the GOPers. Or maybe that's what Kelly or somebody else sold him on. Combined with Trump being upset about his interview, inability to suck his own cock, etc.
Now, I'm being overly fair there to Trump as a manager just to illustrate the point, I want to stop for a second to say I'm not trying to give the impression that he's competent, remember I proposed writing about how The Apprentice explains everything that's happened so far, and I'm not exactly seeing much deviation from that theory.
Rather I was trying to place him in the context of other Presidents of our era, Obama reorganized around the edges and then sent Rahm packing to Chicago in exchange for Bill Daley and a future second round pick. Clinton had to get bailed out twice in his first two years due to poor staffing choices, including bringing David Gergan of all people in to save things the first time and then shunted out everybody for Dick Morris before doing another purge as impeachment loomed. Carter tried to be his own chief of staff until it collapsed and he was forced to essentially rebuild his entire cabinet. LBJ had to deal with the fact that JFK's people were in place and he had to push them out somehow as they were not allies, then he ran into the problem of Humphrey in his final days. JFK tried to staff up with people he liked but then realized he needed people who could tell him things he didn't want to hear. (Though he never lived to figure out that RFK acting in two roles was a problem.)
Nixon avoided this in two ways, he was beyond paranoid as fuck and set everyone against each other from the start, and the GOP was so happy to finally be back in the White House after years outside it (barring the Eisenhower interregnum) that people signed up to be abused. Ford had to do something similar to LBJ in that he needed to get rid of Nixon people and put his guys in like Cheney and Rumsfeld but at the same time, some of the various positions were not entirely Nixon loyalists, plus he had Nixon trying to push him out for John Connolly. Like H.W. Bush he ran into issues of trying to staff his re-election and his White House.
Reagan's staff management was actually based around chucking out people after two years or so. This was half Reagan and his circles own style and half how they shifted from domestic to foreign to domestic, etc. policy focuses. (Which drove Thatcher insane according to her memoirs.)
And all those people were normal politicians who had either been in Washington for a long time or been state executives. Trump's experience for the last twenty years has been entirely different from the twenty before them, and none of them have been like any President we've ever had. The Carter comparison is one I actually like from a certain perspective, Carter came in assuming he would just handle everything because Washington was a joke and he knew better. So did Trump. Carter alienated everyone in Washington and took forever to realize that as much as we hate them, there may be good reasons that certain things are done a certain way in Washington. The chief of staff position was Eisenhower importing his military experience, BUT, it was also on his familiarity with Truman and FDR's chaotic White Houses (FDR's by design) and Truman even later expressed that he wished he had thought of it as he wasted so much time dealing with stuff he should have never been concerning himself with.
Anyway, just some stray thoughts, and I again want to emphasize I'm not trying to argue for/against this or Trump, just that historically it's not really out of the ordinary for these shuffles even this early in an administration. Especially considering Trump was operating with two chief of staffs in Priebus and Bannon. (Not to mention Kushner.) W. Bush did something similar with Rove and Card but he clearly delineated their lines (Rove = electoral politics, Card = executive branch) as to where they had authority until Card left and Rove tried to enlarge his power base and it backfired. Trump never did anything like this, and by all accounts pushed out Priebus (who he never trusted) except for the title to lean on Bannon. Kelly, I have to assume took issue with this nonsense, and I'm assuming that Bannon may have even realized and suggested he could be more effective (or at least make money) on the outside. Especially since he had to know Trump was likely to side with Kelly.