Is it permissible to supplicate with the wording: "O Allah, distance me from so-and-so, as far as the heavens from the earth, because she is a source of harm to me"?

It is permissible for the wronged person to supplicate against their oppressor. Your statement in the supplication means that you are asking Allah never to encounter the person you are supplicating against due to the harm they inflicted upon you. The intention is that Allah separates them from you as far as the heavens and the earth, and there is no problem with this meaning. The wronged person must be just in their supplication, and it is better for them to be patient and not supplicate against the oppressor. We advise you to supplicate that Allah saves you from their evil and grants you victory over whoever wronged you.