Yes, a lie of omission is a lie. However, the situation with Batman refusing to save Ra's al Ghul at the climax of Batman Begins does not parallel a lie of omission.
First of all, it is not universally the law that bystanders must render aid. Secondly, where it is required that they do, generally the law is that bystanders are required to render aid only when they are not themselves endangered. By any definition applicable to ordinary people, saving Ra's from a falling train car would have been a dangerous act. Despite his extraordinary abilities, Batman would not be legally obligated to save anyone in such a situation.
As far as the moral question is concerned, at least with respect to the purported parallel with a lie of omission, there is no parallel. Ra's was in a trap of his own making, and the lethality of that trap was a result of the lethality of Ra's own plan for Gotham. In order to parallel a lie of omission, so that there would have been a moral obligation for Batman to act, Batman would have had to have created that trap in the first place, which he didn't. Only if Batman had created the trap would refusing to save Ra's from the trap be equivalent to killing Ra's.
About all that can be said of the actual situation is that Batman failed to live up to any higher standard transcending ordinary moral codes, under which a person heroically acts to save a life even at mortal risk to themselves. But Ra's was not an innocent victim of a criminal, and saving Ra's would likely have cost innocent lives down the road, given Ra's' stated plan for the city. Were those innocents who Batman might not be able to protect Batman's to risk as well?
Not only that, a lot of Joker's henchmen are blown up by the Batmobile's bombs.
