I'm a little confused.

In the second panel, Haruhi says 有希にみくるちゃん.
Is she literally asking Mikuru to sit on top of Nagato? Or is this some use of the particle に I'm not familiar with?

If it's the former, I guess that explains the punchline, but if it's the latter then I don't really get it.

I'm fairly sure the sentence:

有希にみくるちゃん席に着きなさい！

Was actually supposed to read:

有希とみくるちゃん席に着きなさい！

Making it obvious that she was telling them both to take seats, so I've changed the translation to reflect that.

I don't really understand the punchline either. If it is related to that sentence, then I might be wrong, but at least it sounds better than before.

I had it translated that way initially, thinking it was either a typo or a usage of に I'm not familiar with, but in light of the punchline I went back and revised it.
After all, I wouldn't put it past Haruhi to tell Mikuru to sit on Nagato.

On the other hand (and this just occurred to me)
If you look in the first panel, Nagato is on the left, and Mikuru is on the right.
But when they take their seats at the table, they've switched positions. It would have been easiest for them to take a seat on the side of the table where they already were, with the joke being that they intentionally went out of their way so Nagato could sit next to Kyon and Mikuru could sit next to Koizumi.

In fact, I'm pretty sure that's the intent of the punchline.
I still don't understand the usage of に in the second panel though. Unless it really is just a typo.

I'd say you're right. The joke is that they went out of their way to sit by their "companions." While it is cute and I like the comic, I'd say it failed to make the reader realize this. We see Nagato and Asahina, but their original location isn't stressed. We see them get up and sit down elsewhere, but there isn't really enough of a focus to make us realize the punchline right away.

Ah, good point. I was thinking of the comic as a lone entity, but forgot it does have text related on the site. But, I'm hardly an expert on comic analysis anyway.

Anonymity said:
with the description on pixiv and the last bubble (translations dont always fully convey the original context, and this is one of them) its possible to make the reader realize that

I changed my original translation of the last bubble once I realized what the joke was.
But even after reading the artist's notes on pixiv, the joke still wasn't immediately apparent to me.

Slightly late to the party, as it were, but yes, one can use に to mean "and" in some cases.

Moonspeaker said:
Slightly late to the party, as it were, but yes, one can use に to mean "and" in some cases.

Would it be similar to まで in cases like this?

Ralen said:
Would it be similar to まで in cases like this?

Not that I've seen, no. Well, maybe までに, in the sense of "and even", but not always.