As I noted a few months ago in a discussion of the season premiere of Terminator: The Sarah Connor Chronicles, I have a problem when writers write themselves into situations that they can't get out of without having one of their characters do something against that character's grain. When you're making a show about bad guys and good guys, there's a natural tendency to want the good guy to capture the bad guy; however, doing that means (obviously) that you're going to need a new bad guy on the show, and producers don’t necessarily want to introduce a new character when the old ones are working so well. Consequently, they write themselves into a corner. It's distressing.
It's also, reading that above paragraph, quite confusing if I don't use specifics, so let's take a look at last night's Heroes. HRG (Noah Bennet if you prefer, but I don't), the good guy, wants to take out Sylar, the bad guy. Sylar has terrorized HRG's family, done horrific things to HRG's daughter, and just been a generally bad dude. HRG, in addition to wanting to protect his little girl, actually gets paid to take out bad guys like Sylar, so he has a double-motivation in going after season one's Big Bad on a repeated basis.
Last night, HRG actually caught Sylar. Better than that, there was an eclipse, so Sylar was completely powerless. In a move showing that HRG isn't your 1950s-style good guy, but rather more of a modern day, dark, conflicted hero, rather than taking Sylar back to Primatech's jail, HRG just opted to slit Sylar's throat.
Oh sure, at first blush, that seemed like a perfectly reasonable action – Sylar being an immensely bad dude and all – but it wasn't. Sylar may not have had his powers at that exact moment, but we already knew that Bennet was betting on a return of powers to the superfolks – hence his suggesting that his daughter need not go to the hospital for a gunshot wound (he figured she'd be able to heal herself when her powers returned).
So, a simple throat-slitting wasn't really a reasonable action at all. It, thought of superficially, satisfied the audience's desire to see good triumph over evil, but really looking at the event it becomes clear that it was out of character for HRG to only slit Sylar's throat. There was no way that such a simple single injury would have kept Sylar down in the long term and HRG should have known that. In fact, I'd argue that if the writers had been true to HRG's character at that point they would have had him decapitate Sylar (always a sure-fire way to end a bad guy, provided the head and body are kept a large distance from one another).
However, the writers didn't do that. They tried, instead, to satisfy both the audience's desire to see the bad guy “get it” and a general desire to not have to introduce a new villain when the current one remains so popular (because, let's face it, Sylar is a guy you just love to hate). It simply didn't work. HRG is smarter than he acted last night; he knows far more about folks with superpowers (even when said superpowers are temporarily gone) than he demonstrated by only slitting Sylar's throat.
Admit it, if you were watching you knew that without a decapitation Sylar would be back before the episode's end and you were yelling at HRG to inflict a more permanent sort of death on the villain. It's okay, it doesn't show some sort of bloodlust on your part, just a deeper understanding of the world.