If you turn the mages over, Anders, Bethany and Merrill will get pissed, but Aveline, Carver and Fenris will approve. If you promise to kill Thrask, you'll get some points from Anders, neutral from Bethany, and negative points from everyone else. You'll get points with Merrill if you say "I'm sorry" when you're talking to Grace after killing Decimus. You'll also get a bonus item, the Chantry Staff, if you help the mages. If the mages go to the Circle, you'll get the Bounty Hunter quest from the Chanter's Board in Act 2, and if the mages go free, you'll get the Search and Rescue quest in Act 2. If you do kill Karras, you'll unlock The Midnight Meeting quest in Act 2. Use Varric if you're trying to avoid a fight with the templars and killing Karras.
You can lie to Thrask and say they're all dead, and again you might be able to avoid killing Karras.You can avoid fighting Karras with this option.