A lot of it was awkward, almost as if the producers thought 'we're going to get savaged for this episode if we put the Saville stuff in, so what the hell'. Whilst I didn't think the Abu Hamza joke was funny, I think it was worth saying because he deserves contempt. I don't think the joke was intended in any way to make light of 9/11 or its victims, quite the reverse. Likewise the Justin Lee Collins joke was intended to skewer him, not make light of his abuse.
I thought the episode was good, given the subject matter in the news this week. They have to keep it to whatever is topical and if they hadn't mentioned JS then That would have looked phoney and cowardly.
I think Mock the Week basically avoided the Saville story. They were more compelled by wanting to set the record straight for themselves, rather than commenting on it as a new story. Which I think is reasonable.