(For the purposes of this answer I am assuming Data and Lore are sentient Federation citizens. This is not meant to contradict @N_Soong's answer; I agree with that answer. I'm exploring some of the more subtle legal and moral issues of Lore's detainment.)
Would it be murder? No. It's not even analogous to murder because Lore can be reassembled and reactivated. It is extreme detainment. What is in question is whether Lore's right to due process has been violated.
Lore is detained... but disassembly is more than detainment. It would be like keeping a prisoner in a perfect coma. Yes, as a Starfleet officer Data in the line of duty could subdue and detain Lore. Data could recommend to Captain Picard that Lore is an extreme security threat and that he be disassembled. Same as they could keep a flesh and blood prisoner knocked out for the voyage. That part is fine.
Once safely back at Starbase, Picard would have to turn over Lore to the proper Federation legal authorities to decide what to do with him. If they failed to do this, then Picard and Data would be guilty of holding Lore indefinitely without trial.
If the Federation did not ever revive Lore they would be guilty of violating his right to a speedy criminal trial. If they tried Lore without reviving him they would be violating his right to know the charges against him, his right to call witnesses, and his right to choose counsel. (These are all based on the 6th amendment to the US Constitution, but they're universally applicable and I'm going to assume the Federation has some version of). Only after having done all that would the Federation be in the legal and moral right to decide Lore's fate.
If Lore's deactivation were permanent then it would be analogous to death. This death happened after Lore was already subdued, defense is not an argument. Assuming the Federation is using definitions analogous to US law, Data killed Lore with [malice aforethought], it wasn't an accident, but it was not premeditated so it could qualify as second-degree murder.
However the extenuating circumstances match the definition for the lesser charge of voluntary manslaughter: Data was provoked by Lore, Data believed he was acting in self-defense (that Lore was too dangerous even disassembled), there was no prior intent to kill Lore, and it was not while committing another felony. The qualification that the circumstances would "cause a reasonable person to become emotionally or mentally disturbed" would be very interesting to argue in court for Data.
Some people have raised details like Lore's criminal insanity ("malfunctioning"), his crimes, and his relation to Data all as justification for allowing Data to make the decision to kill or permanently disassemble him. None of these are justifications. Let's deal with them one by one.
Lore and Data are "brothers"! That works fine in fantasy stories, but not in a civilized society. Your family cannot judge whether your are insane and dangerous, that is up to a court. They can initiate the process, but ultimately a court decides. Why? Because you're not the property of your family and your family cannot violate due process.
But Lore was really dangerous! This works in action movies, and it justifies the extreme measures of imprisonment (disassembly) Data recommends, but it doesn't justify killing Lore once he has been subdued nor indefinite detention. No matter how fantastic the charges, Starfleet officers are not judge and executioner. They have subdued Lore, he is no longer a threat, and now has the right to trial. Even criminally insane mass murderers get due process.
But Lore was insane! This is not for Data to decide. Once Lore had been subdued the question of his mental state is handled by a court appointed mental health professional (or positronic brain expert I guess). Even if that had already been done, killing crazy people is still murder. Alternatively Lore would have to have consented, a court would have to agree Lore was able to consent (ie. that Lore wasn't insane... which he was), and euthanasia would have to be legal.
But the Federation was at war with the Borg! Were they? When was this declared? Data doesn't get to decide they're at war, the Federation council does. Let's say the Federation was at a state of war. Lore is either a Borg soldier in uniform, or a Federation citizen fighting for the enemy, or probably both. Once subdued, he is either a Federation prisoner of war or a criminal, probably both. Either way, Starfleet officers don't get to perform battlefield executions of prisoners.
In the end, we do not know what happened to Lore after Data disassembled him. He could have undergone a fair trial, which would make everything Data and Picard decided to do moral and probably legal. If, as one novel says, he was dumped and forgotten in the Enterprise's cargo hold that would leave Data and Picard on very shaky moral and legal ground playing judge, jury and executioner by detaining Lore indefinitely without trial. It also means Lore crashed with the Enterprise on Veridian III possibly to be found and assembled by someone else. Maybe a vessel that regularly sees combat and dangerous situations isn't the best place to hold one of the most dangerous criminals in the quadrant: sloppy.