Pulling punches? Screw that. I certainly wasn't in that fight, and most of you weren't there either, but I can come up with multiple reasons right off the bat for nuking the sword and not the fighter:
1) Charm Person/Monster -- Yes, I know you'll only have your backup weapon, the +1 Heavy Flail, but I'm sure the party rogue will be occupied for a few rounds nevertheless.
2) Interrogation -- Who are you, who do you work for, any chance you'd be interested in accepting a geas to go and kill the people who led you here in return for your life?
3) Loot -- He's wearing a ring of WHAT? I'll just dust his sword and then missile him to death. Because I WANT that ring.
4) Positioning -- Oh, please, tanklike warrior, please, whatever you do, don't come up and stand directly in front of me and pummel me with your much less effective backup weapon and incidently position yourself so that the party wizard can't catch me in a fireball without catching you too. (Weak? Yes. Possible? Also yes. If he's got Stoneskin and good Concentration, and some defense against getting grappled, having a Live Fighter in front of him providing unintentional cover could be valuable)
5) Actual Mercy -- My cause is truly just, and I would in sooth not slay these poor misguided souls when I know that my sweet rhetoric, combined with the hypnotic properties of the Gem of Ilyana, can sway them to my noble cause.
6) Megalomaniac -- I WANT HIM ALIVE, bwahahahaha! (This one is absurd and stupid, but it happens in so many movies that it's an official cliche, and as such, allowable)
Three fairly weak reasons, which only work if you've really established the guy's character beforehand, and three reasons that any PC should understand.
-Tacky