I think that the situation in #49 actually proves that David was not able to contact the yeerks. David knew all of their names, their addresses, everything, but in #49 the yeerks were still searching for them. When the Anis got into the base, the yeerks had only found Tobias's mother (who David didn't know about), and it was implied that that happened very recently. If David got in touch with the yeerks, they would never have run the DNA search program at all. Before the Animorphs knew anything, the yeerks would have stormed their houses, infested their families and, if possible, infested or killed them.
That said, in #48, David had recruited two "henchmen," who saw Rachel morph multiple times, and managed to escape at the end of the book. If they talked about it, that certainly could have tipped off the yeerks that the Anis were human. So it might still tie in, in a way.
The one scene in particular that makes me think of this is in #52, when she goes to kill a controller even when he is trying to escape the war and trap himself in a bird morph.
I'm pretty sure that the controller only told Ax that he was trying to escape the war. If I remember right, Rachel didn't come in until after Ax had let him go, so she probably didn't know what the controller was planning to do.
On topic, I think that Rachel did kill David. I don't have any particular reason, it just feels like it would fit better than the alternative. And, like I said, we know that David did not get in contact with the yeerks.