I think your professor excersized very poor judgement.
1. he gives his students the impression that ddos attacks are ok if you can justify it to yourself
2. the attacker now has the addresses of enough machines to launch his own attack PLUS the machines are on a network that you know he can gain access to.
3. Your professor does not know what service or machine he took down and by taking said machine down, he makes the task of finding how the attacker infiltrated the network more difficult.
4. Your class may have taken down a completely innocent machine. Things as simple as uncontrolled ping requests have been mistaken for attacks before. If this were the case, it would have been you guys who been in the wrong.
Overall, I'd say he should have acted a little more responsibly.