Autotune in graphic mode or melodyne
if she's really that good that it even wasnt that audible during recording then you shouldnt have problems tuning only those parts that are a bit off, without making it sounding unnatural.
just edit those parts that need it. you dont even need to snap it 100% on the grid, just experient were it sounds good and leave it at that.
When singers are REALLY good you sometimes have the problem that some notes sound extremely off, because they are THAT accurate normally.
so when you open up the pitch correction and analyze it you see that its not even that much off, but its a lot more audible because the rest is so perfect...if that makes sense?
at least that was the experience with my bands singer.