If they were considered dead, then they never could have been brought back in the first place. The show starts off with the EMH saying that he can find a way to separate them to bring them back. The chief medical officer didn't consider or pronounce them dead, then there is no reason we should.
So if someone is lost in a transporter snafu, when do you declare them dead? Their signal merged to become an entirely new signal- a new lifeform. At that moment they ceased to exist. The doctor may not have declared them dead, but since their transporter patterns were lost and their matter destroyed and reconstructed, they were biologically dead.
Plus, the doctor, like Janeway, was emotionally compromised as the individuals were his friends and persoanl patients. Just because he didn't want to declare them dead, doesn't mean that he shouldn't have.