It's a tribute to either how subtle a writer Martin is or how knackered (and slightly drunk) I was as I watched the episode that it took me a full three days to realise that he had.
Indeed, it's genuinely surprising how few people online have grasped what really took place in the Stark tent. Letting that Lannister spy go was only merciful in the sense that killing him certainly wouldn't have been. Beyond that, though, and it's all tactics. Hapless Enemy Spy #1 isn't going to be the only spy in the hills, but now not only has he handed Robb an extra two thousand warriors, he's had that number confirmed by the enemy general himself.
In other words, mercy can be a wise policy, or a foolish one. Or something to be ignored, or something to feign in the more general scheme of things (as evidenced by the Small Council hold its possibility in front of Sansa like a baited hook). I've noted before - as have many others - that the overall theme of this season is power; its acquisition, its retention, and its application. Who deserves power, who can sensibly wield it, and the degree to which those two things coincide.
And mercy, of course, is an appliance of power like anything else. As usual, Martin has no intention of commenting on the morality, wisdom or pragmatism of any one choice over any other. Once again, what is, is.
So no. I don't think his script was really all that different from his book at all.
Update: Gah! I got out my copy of A Game Of Thrones yesterday to check through Syrio's fight with the Lannisters, but I still managed to miss the fact that the line about not running is in there! I don't think that mistake really makes a difference to my overall point, but it's bloody annoying.
 In fairness, I haven't read any of the original books, so I'm relying on the reports of others for this one.