Krakauer asks: "if Ron Lafferty were deemed mentally ill because he obeyed the voice of God, isn't everyone who believes in God and seeks guidance through prayer mentally ill as well?" [p. 297] Given the nature of, and motive for, the murders of Brenda Lafferty and her child, should Ron Lafferty be considered mentally ill? If so, should all others who "talk to God" or receive revelations—a central tenant of Mormonism—also be considered mentally ill? What would the legal ramifications be of such a shift in thought? Any thoughts on this?

Ron Lafferty's total willingness to violate secular laws to fulfill what he believed to be the will of God sits at the heart of a major dilemma presented by Under the Banner of Heaven. And while it is presented here within the context of Mormonism, it is not unique to that religion.
In general, modern society has accepted the notion that speaking to God is normal, while God speaking to you is abnormal.
The question here has less to do with the classification of mental illness and more to do with the state's responsibility to restrain crime. In other words, a person who claimed to hear the voice of God may be mentally ill, however, mental illness is not itself a crime. In the Lafferty case, the evocation of God's voice inspired an act of malum in se ("evil because it is"). These are acts such as murder and rape that are inherently unlawful because of a societal belief that they have transgressed a higher order, such as a heavenly commandment. They can be contrasted to acts of malum prohibitum ("evil because it is prohibited"); those acts which are wrong simply because man has deemed them to be—crimes such as poaching and espionage.
Because society has determined that God has outlawed acts of evil, a person who has heard God command him to do evil must be, by matter of course, deluded. Therefore, there is no reason for the legal system to be too concerned about others claiming to receive revelations unless they receive revelations that are demonstrably false. An order to commit malum in se is demonstrably false because "it is" inherently evil.
The second part of the question asks what the ramifications would be if the law began to classify all persons who heard the voice of God as mentally ill. In general, there would be little ramification to such a classification because, as previously mentioned, mental illness is not itself a crime. The Lanterman–Petris–Short Act, and similar legislation inspired by it, generally restrains the state from interfering in the lives of the mentally ill against their wishes.