Because they never really wanted to kill the Visser. In the early books, it was because he had Alloran's body. If you remember, Ax attempted to take his life, as well as Alloran's own brother, but couldn't bring themselves to do it. Cassie said, "As long as there is life, there's hope."
Mid-series, they didn't want to kill Visser 3 because, as Tobias said, it was a case of the devil you know vs the devil you don't. They had realized that killing the Visser would accomplish nothing and might actually hurt them if a smarter Visser replaced him. Either way, the war wouldn't end because of the death of one yeerk.
In the later books, reason #2 didn't apply, but they still didn't prey on him midmorph because Jake wanted to retain some semblance of honor. He made the new Animorph motto "Fight the yeerks, don't become them."
In the end they freed Alloran so I suppose it was the right thing to do.