I don't quite get this "transcended his programming" thing. Should we really think that Data was born with some sort of a "no kill I" rule? If so, he had "transcended" that aeons ago: he was a Starfleet officer whose duties included murdering the enemy for king and country. By the time of "The Most Toys", he had pulled the trigger on the enemy with lethal intent in at least "Q Who?" and "The Survivors", and had engaged in potentially lethal firefights in half a dozen episodes. No doubt his previous Starfleet career and training had already required him to come to grips with the idea that he would take lives as a matter of course.
As for lethal intent in "The Most Toys", we have to separate between whether Data wanted Fajo dead, and whether Data wanted Fajo stopped. Data could choose whether or not to stop Fajo. But if he chose to stop Fajo, he could not choose between lethal and nonlethal means, since the only weapon he had in his possession was lethal in all circumstances. (He might have simply walked over to Fajo and snapped all his limbs without killing him, but an energy weapon would be his only hope of coming out of the fight alive in the long term - Fajo had a largely loyal and supposedly armed crew, after all, and Data was alone.)
In other circumstances, Data could quite well have stopped Fajo from being a danger to life and limb. There exists an efficient system of criminal management in the Federation: Fajo would either be quickly rendered harmless by advanced psychotherapy, or then locked into a mental asylum for life as an "incurable case", as shown several times in TOS. Logic would thus not require Data to kill Fajo.
To examine anger and vengeance as Data's leading motivations is an entirely separate issue from pondering whether Data's logic required him to kill Fajo. Nothing elsewhere in TNG suggests that Data would have been able to actually feel anger in that situation, not unless augmented by the emotion chip - but there are many instances where human customs and exceptional circumstances confuse Data's generally utilitarian logic. The supposed "outburst of anger" in "The Most Toys" could be explained either way: a logical act in Data's rare predicament where he only possessed a lethal weapon and had no backup, or a rare breakthrough/lapse into emotion that he later carefully covered.
Personally, I prefer to think it was the former, as that's more consistent with Data's earlier and later portrayal.
Timo Saloniemi