This is singularly the most wholesome, amazing ending of a failed ship I've ever witnessed. Think what you want, there are some people you simply can't think about romantically, even of you do care for them. Tsubame with Ishigami is a prime example of that. And thinking about how to let down someone without hurting them is a Catch 22: virtually impossible to do. If the guy has any sense, he won't stay around the girl who rejected him yet still has feelings for. But that is exactly why Tsubame feels it so bad, since so many of her close guy friends leave because of it.
So, that's why she tried to placate him, even going so far as offering him a one-night stand, because she genuinely didn't want a friend she cherished to leave over feelings she just couldn't share.
Of course, that all hit Ishigami like Truck-kun on the first episode of an isekai. He genuinely had feelings for her, and feelings that intense never go quietly. If he has any self-preservation instinct, he'd try to keep a safe distance between him and the girl who rejected him, but Tsubame admittedly asked him a selfish request to stay friends together. It's not impossible, but it's going to be real hard, and I'm confident that Aka-sensei can successfully pull this off.
Also, props to Glasses Girl (I'm really sorry I can't remember her name) for having hope for my man like that, she's a real bro. Sensei really knows how to write compelling, platonic relationships between the opposite sex, in a genre were it's almost a given that any relationship like that would turn romantic.