What took you so long? (Asks for the reason for the delay. Why have you only just come? is grammatically perfect but not to the point.)

"why have you only just come? " = the natural way a native would say it. The "ONLY just come" emphasises that the friends came back a long time ago but the person in question "has only just (now very recently) come back".

It isn't wrong, and I can see a native speaker saying it. I would strive for more clarity. Something like: *Why did you come back only now? *Why did you just arrive now? *Why didn't you come back until now? <---my favorite and clearest *Why did it take you so long? <--very common and idiomatic *Why are you only just arriving now? The real question in this context isn't why are they arriving NOW, but why DIDN'T they arrive earlier. When I saw the title of your question ("Why did you just come?") I thought the context could be "Why did you just come and not also bring a dessert and a present?" : )