Can "to settle accounts" be used in an extremly minor business?

You order online a book (only worth 5 dollars) from a bookshop, and the dealer tells you that an extra 1 dollar will be charged due to the increase of shipping fee. Can you reply with "Okay, to settle accounts"?

No, and I'm not sure what you mean to say. It almost sounds as though you're saying that the extra charge annoys you so much you want to settle all your oustanding amounts due so you can close your account.

On the other hand, to settle your account, you have to pay what's owing even if it's only one cent. If that's what you mean, yes, the phrase relates to accounts of any size. It's also used metaphorically, and as such, can also be used for any size of issue.
Metaphorical: "X feels he has to beat Y in the race to settle accounts for last year (in which Y beat X)."

Whatever your intended meaning was, "Okay, to settle accounts" is not a correct English sentence.