I think I would re-sing in it, and try to get it right. And skip the Auto-tune entire. I've re-sung a lot of stuff until I got a take I could be happy with. Using Auto-tune is anathema to me on vocals. (I don't have Antares Auto-Tune, but I do have Melodyne Studio 4.) I have three singers I'm recording right now, and last week one of them sang flat on a verse. I pointed this out, and she re-sang it, and nailed it. I tell them that I don't tune vocals, except under extreme circumstances. All three singers are good, and they will only get better if they strive to get it right. Auto-tune is used almost universally at this point, even on singers who don't need it, or shoudn't need it (like Adele). It's just a weird modern thing.
I ain't sayin' don't use it. I'm just saying try to get it right without it.