Our nonprofit hired a non-resident in 2016 on a J-1 visa and the arrangement was that we would pay her income tax. She is now back in her home country. We filed her return. Turns out we owed money, so we just paid it plus the small penalty and interest. The check has cleared the bank. However, I'd really like to have a confirmation that her account has been credited. Looking online, it doesn't seem like anyone can do that but her given the list of required information needed to open an online account. I get this in that there could be a lot of fraud otherwise, but does anyone know of a way I can get a confirmation that her account is good and that there is no balance?
If you want an "account statement" from the IRS listing the taxes due and paid and confirming a zero balance remaining, you want what they call a Tax Account Transcript. It sounds like you tried to submit this online, but yes, it would require the actual taxpayer to submit it. The other option would be to fill out Form 4506-T requesting the Form 1040 Tax Account Transcript, have the taxpayer sign it, and mail it in. Presumably whatever method you used to have her sign the Form 1040 you prepared for her you could also use to have her sign the 4506-T.
Another option could be to try to request the transcript over the phone. I don't know what authentication they require, or if you would need to have been listed on the 1040 as an authorized Third Party Designee. According to the IRS Transcript FAQ Page:
Q19. What if I’m unable to use Get Transcript by Mail?
If you are unable to use Get Transcript by Mail, you may try our automated phone transcript service at 800-908-9946 and also receive your transcript by mail. Please allow 5 to 10 calendar days for delivery.
But unless there's a reason to think that the tax account wasn't credited properly or the IRS is sending another bill or the like, I don't think there's a lot of point in doing so. In general, the fact that the check cleared the bank should be sufficient documentation that the amount was paid.