[SlipperyJim]

OmikronWarrior and archaeolept are right. The best way to deal with a highly-mobile thug or SC is to whack him before he can move.

The problem is that most thugs (and all SCs) have high magic resistance and strong defense, so most assassination spells (Mind Hunt, etcetera) will be iffy. Still, I have found that gearing up a "battery" of Mind Hunters with penetration items can give them a chance even against a high-MR target. Rune Smashers, Spell Foci, and Eyes of the Void are your friends! If you have three (or more) S4 mages equipped with the right gear, then you can just keep Mind Hunting until you succeed. He'll fail his MR check eventually....

If you happen to have the coveted Blood-Astral combo, then you can also spam Call Horror rituals at the thugs/SCs. A top-notch SC will probably be able to take a Horror, but a mere thug should be Horror Chow. Fliers are especially vulnerable to this approach (unless they're immune to Fear), because they're frequently behind your lines with no clear path to retreat. Even if the Horrors don't kill them, enough Fear bonus will still make them rout. With no retreat path, a routed thug or SC will simply die.

Another great choice is to Teleport or Cloud Trapeeze your own SCs (or anti-SCs) into battle. As OmikronWarrior mentioned, magic movement happens before "regular" movement -- even against fliers -- so a Teleporter can intercept the badguys before they can move!

There are many customized anti-SC / anti-thug tactics to try. One of my favorites is a little spell called Paralyze. Teleport a couple of Astral mages along with your own thug(s). Tell the mages to spam Paralyze, and the badguy won't be able to fight back. Easy kill for your own thug!

Assassination attempts also take place before the regular movement phase. If you happen to have some really buff assassins available to you (big "if"), then you can place them in the likely target provinces. Wait for the enemy thugs or SCs to fly into the provinces, and then assassinate them before they can continue their rampage! However, please note that an assassin who can stand up to a thug (let alone a true SC) is quite rare, so this option is least likely to succeed.