With Ben's reaction to hearing that John knew about Hawking and wanted to speak with her, it tells me that Ben may very well not be working with her at all. Ben may well have only been using her. Certainly at least he didn't want John to come between him and Hawking.

Still don't believe that either Hawking or Widmore are altruistic, wishing to do some ultimate good, but Ben is ever more certainly the Evil puppeteer in this drama.