Playing it out.

[Telonius]

Here's how I handle it, generally. For all social situations, I let the players play it out first. If the player requests a sense motive roll, I give it to them. If the player doesn't want to use any particular skill in figuring out if the NPC is being honest, I let them react however they want to react. So for the player, it's either trust your own gut and have a 50% chance of being wrong no matter what, or roll the dice and have an unknown chance of being wrong. Besides, if they really think their character wouldn't believe the vizier is being honest, then they'll probably act that way anyway regardless of how the dice fall.

(Side note, I do not treat Sense Motive as being an automatic truth detector. I treat it as being an honesty detector. If the peasant really believes he's been abducted by Mindflayers, Sense Motive will show him as being honest no matter what the roll. A player using the Sense Motive skill would think that he's not trying to milk the story for attention, etc. It's up to the player to determine whether or not the character thinks the peasant is nuts or not.)

EDIT: when the players do call for a Sense Motive check, I always roll the dice, whether or not the NPC is actually being honest. That way they don't know which rolls I'm actually paying attention to. You could also just preroll a Bluff check for all NPCs - doesn't matter which, as long as you're consistent across all NPCs so the players don't notice a pattern.

If the player attempts to influence an NPC into doing something he otherwise wouldn't have done (bluff, diplomacy, or intimidate), I let the scene play out and then call for a roll right before the NPC would react. I assign a bonus or penalty to the roll based on what was just said, more or less like the "bluff" examples in the PHB demonstrate.