El Payaso is right - Batman's decision wasn't fully in line with the morals he had seemingly established... his code, so to speak. Sure, it was a tough call (myself, I would've been torn about what to do, assuming I could've saved Ra's), but that doesn't excuse him. If it's a flaw in the movie or part of character development, or "anti-development" - can't say, but I, myself, will attribute the "flaw" to the fact that this was a rookie Batman.
Imagine that, instead of Batman saying what he said and doing what he did in the movie, our crimefighter had extended his hand, as if inviting Ra's to grab it, and said something along the lines of, "forget what you said about compassion."
That would have been the Batman thing to do... and Hell, it could still have ended up the way it did in the movie, seeing as Ra's could've refused, and that Batman would've felt the need to escape, with or without Ra's. Anyway, it's too late for that now, but perhaps they'll show a more compassionate Batman when The Joker enters the picture.