Sending in the owl is really not much different from sending in any soldier for a behind enemy lines operation.
You could even say it's less cruel and it's definitely not evil at all, in respect to the spirit, as the owl is just a magical spirit which can't really die by this.
Also, consider that Dan is playing a vengeance paladin and, I believe, scourge aasimar.
By that alone he's more akin to the fountains hit squad than a noble knight.
He's still not exactly good, but if he assumes this town is more or less completely criminals then he's just delivering justice. To call him evil we'd need to see what he'd do if the enemies would, for example, surrender
The wyvern venom wasn't likely to actually kill anyone either, just "poison" them and creating a combat advantage like that doesn't conflict with vengeance pala at all.