Based on my experiences with the system so far and that is by no means extensive... but you can play an Intimidation three different ways, the first method is using it to play a maneuver on the thugs we will call it "Riddled with Fear" that she could tag for free on any of the thugs or pass to the Wizard.  The second way and the one I believe you used is intimidating them so badly that they have to roll to even act against the character, and that is a Block, with the Block Strength being what they have to roll again.

The last method and the one that seems most supported by the rules is that Intimidate is a Social Attack (See the Intimidate skill and the Social Attack trappings). It does Social Stress. They would have likely been taken out all the same as if it was a Mental conflict, and if they were taken out then the Meteomancer gets to describe (with approval from GM as its a give and take thing) how they were taken out.

Also... everyone always has 2 stress boxes for each physical, mental, and social if they are low-threat thugs and don't take consequences then any attacks over 2 stress will take them out. They get more for having a higher skill in Endurance, Disciple, and Presence.

As for the zone-wide effect I would follow the rules under magic!

Fate Points in general spent for combat are just crazy. I have a Pure Mortal character in my game... he has 3 stunts and 9 fate points... tonight he told an big gruff not to start a fight in the middle of the street (not the elder gruff but the big ones right before him)... the gruff did not listen an smacked at the Champion of God for retribution for one of his brothers... he stabbed him with iron knife for a 2-stress attack in response, the Gruff turned on him and told him that he would dance with the little mortal, and so the character pulled out his .44 revolver and tagged every one of his aspects using 5 fate points... his guns is +5, +12 for aspects, and +2 roll... 19-effort attack vs the gruffs +2-effort defense roll... 20-stress damage from a Pure Mortal!!!... all my PCs fear the Pure Mortal because of the amount of Fate Points he has...