Note that the requirement for getting the full "Clear outpost without getting seen" bonus, is that they don't see you (this includes guard dogs, by the way). It doesn't matter how much they hear from you, your rocks, your guns and your explosives. Also, the alarm will only be triggered after a soldier saw you with his own eyes. You can make as much noise as you want, as long as they don't spot you. Yes, that's right - you can clear out an outpost by bombarding it with grenades and RPG rockets from a nearby cliff, and still get the 1500 exp bonus.
When you still want to take out the dogs without making a sound to avoid alerting the guards, there are silencers for most guns available (not just for pistols, but also for SMGs, some assault rifles and even for sniper rifles), and there is the recurve bow.
During most of the game, I always tried to carry at least one silent long-range weapon (sniper rifle or bow) and one silent automatic weapon (smg or assault rifle).