A lot of people got angry with Naomi for her decision to try to deal with Marco and Filip alone, sans Holden, and I get it. But its easy to look at this from the outside and judge her. It's harder to try to put yourself in her shoes and empathize with her decision, however wrongheaded it might be.
I think what was driving Naomi's decision had a lot to do with politics and guilt. Naomi left the belt, and "her people" years ago for a life of relative privilege, first working on the Cantebury, and then joining the crew of the Rocinante to go tooling around the solar system (and now other solar systems as well) being the Big Hero. It's objectively admirable, but taken from the perspective of the Belters she left -- and there's some of that thinking ingrained in her psyche as well -- it can be seen as a selfish act of betrayal. There is, of course, more to the story, as we already know, and as we will see in even sharper focus as the season progresses. But most people don't know that. Most rank and file Belters probably see Naomi as someone who ran away at her first opportunity to seek a better life, because she could. She turned her back on her people and went to work for their oppressors. This is how she's viewed, and while some Belters probably admit that they'd do the same thing if they had the chance, many others see only someone switching sides. To the *wrong* side.
So Naomi has some of this in the back of her mind, as well as guilt about leaving Filip. "If I had stayed," she thinks, "maybe I could have kept him from having his mind poisoned by his father. Maybe I could have even gotten Marco to tone things down a little and see reason." Of course this is revisionist thinking, and of course it's irrational, but guilt rarely is clear-eyed or rational.
So the part she tells Holden is the political part -- she can't show up with him in tow, because it will just make the job she's trying to do harder. And that's true, but it's only a part of the story. The part she doesn't tell Jim is the not-so-rational part, the part about how she can't help but feel that she made a selfish decision back when she left, and that now she feels like she has to clean up the mess she thinks she made without having James Holden there to interfere, or be a crutch, or talk her out of anything. She feels like she has to make amends for her transgressions, imagined though they may be, and she's not going to let anyone stand in the way of that.
As I said, it's not rational. But it is what she feels, and it is very human. And, at least for me, it's not that hard to understand.