It was like the equations had turned now. While Lia believed Azekiel before and Raphael didn't, now it was Lia who didn't believe him while Raphael wanted to listen to what he was saying.
Raphael knew that if Azekiel wanted, he could've lied about many things. He could've lied about not creating the Tower as well. Why would he accept the truth? If he had lied, the two of them would've believed him even then. If he told them the truth, then maybe he really didn't want to lie.
If he was telling something, Raphael believed that they needed to give him a chance. In any case, it wasn't as if they could do anything else. They couldn't hurt him since they were bound by the rules of the Tower, which didn't allow them to attack their Summoner.
They were at Azekiel's mercy even now. Moreover, Azekiel didn't look like he was lying. At least Raphael couldn't see it.