Why kill spies? I would think turning local spy in to double agent would be far more beneficial. Or at least feed them wrong information you want. Killing spies simply replaces them.
The second you go after anyone using the communication channel it's fairly likely the entire channel will shut down or change so you're much better off moving quickly on everyone you identify than leaving them out where they might disappear. This is especially true since the information China used was provided by Iran - so was very likely to leak sooner or later. Once you've rounded up all the spies it's up to the government what to do, but either they can trade them, imprison them or kill them and I guess this time they decided it was best to just send a message.