Even if there is a bigger reason for wanting her out, there is no reason for them to expose PRISM that way. Immigration officers already have rights to deny anyone without explanation.
I just don't find anything about that article logical.
This particular case, if true, may have nothing to do with PRISM. A simple search of communications between the person and only her US contacts would probably result in a small amount of data to search, which could probably be obtained by DHS or CBP via the providers directly.
I just don't find anything about that article logical.