It's not "without" so much as it is "putting to the side".
馴染む doesn't have to be a positive thing. In fact, I thought なれなれしい was a good thing until I continued to hear it in negative circumstances. It seems like you'd want to be close to someone, but the sense is more acting like you're friends even though you haven't known each other long enough to actually be friends. It has a sense of imposing.
If it weren't for all that comes before it, i.e., 住むのは親戚でもないきりしまはるとの家!つまり居候!"会ったこともない奴が、いきなり自分の家に住むなんて。。。。"納得いかないはるとをよそに... I'd probably have no problem agreeing that 馴染む is a good thing, but in this context, it certainly doesn't seem to be. ...where she's living is Haruto's house, even though they aren't even related! Leaving Haruto aside, who didn't condone, thinking "I'm supposed to suddenly live with someone I've never met?! in my own house??!!"...