I don't think Allen is protecting Cross. Allen thinks that Mana was a normal human, after all - he doesn't want to think of the possibility that Mana was a Noah (which is what other people seem to be trying to tell him). The reason Allen doesn't talk about it is because he doesn't want to think about it, because he will then have to accept things that he doesn't want to.
As for the Noah, maybe it's not good for humans, but it's what God wants - or maybe it IS good for humans in the long run - we don't know. And how concerned must the Order be with saving human lives if they're so willing to sacrifice them? It seems they have another motive.