Look! Up in the sky! Is it a bird? Is it a plane? No! It's Cryptex, Advisor of (Most) Things Jail! Yaaay!
Anyways, onto OFFICIALLY answering your questions, instead of providing hearsay and rumor! Yay!
1. You were not in the wrong in this situation, it was simply a misunderstanding. If you see vents have been opened you are free to go down to the exits to try to cut off escaping terrorists, and if you see more after you're about to leave, you can finish them off as well, it's their fault for not seeing their friends had suffered the same fate. If you are warned by an admin, simply explain to them in admin chat (Teamchat

Message) what you were doing.
2. The warden cannot pardon wanted T's, they can ask for them not to be killed, but any CT may kill any wanted terrorist as they please.
3. If no CTs that are alive have microphones, any admin will come over chat to give more orders. If there are none in the server, try to find one on Ventrilo or Steam.
I hope these are sufficient answers to your questions. If they aren't, or if you have any more questions about jail or really anything else, please PM me. Thank you!