The St John's Wort is a "kind of" alternative to the pill, in-so-far as it's primarily supposed to be used for mental issues (depression, anxiety and mood disorders etc.) but supposedly also has negative side-effects in regards to fertility, but the main worry about it is negative interactions with other medications, including the pill.
It's possible that if she is taking the pill and St John's Wort knowingly, that she's accidentally overridden the effects of the pill.
I don't think she'd try and hide taking the pill by disguising it as St John's Wort. I can't explain it any better than it seems out of character for her to do that.