My husband has always said there's something untrustworthy about Holly...however, I am a bit on the fence about her in these circumstances. I believe she too was a victim of his cohesive control, in the beginning at least. She probably felt like she owed him a lot given that he gave her his seal of approval to work on This Morning as Fern's replacement alongside him. Before that she's was just a kids presenter. Notice how Phil surrounds himself with weaker women, Rochelle, Josie etc... Amanda Holden and Ruth didn't stand a chance.
Part of Holly probably felt conflicted if she knew about the runner, which in all likeliness she did - if she blew any whistles perhaps there was a fear Phil was untouchable and she feared for her job. She would have also been outing him as gay as at that time he was still playing happy families with the wife and daughters. There's also an argument that the kid was still technically of age... ambiguous I know!
It maybe an unpopular opinion but I don't think Holly is to blame but I think she needs to better clarify her knowledge and position in order to not get dragged down with the sinking ship.