I would contend that Lara sees Harry as a trusted enemy not ally. Someone you know can turn on you, but you also can trust them to act a certain way. In Harry's case, he is a know white knight that has a strong moral compass. Lara knows what strings she can pull to get a certain response out of Harry. It will be interesting to see how this might change in Twelve Months.
It isn't about Lara or Thomas trusting Harry, they can.. It's about Harry trusting them. It isn't a matter of morality either, back to the pet tiger analogy, as much as you love it and believe you can trust it, if it is hungry enough, it's natural instinct wins, and it could eat you. Vampires do what vampires do, that is what Eb is telling Harry. Now whether this is from Eb's own personal trauma, as in one killing his wife, or from the general experience and knowledge of his 200 plus years we haven't been told yet.