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).