The SC were engaged in lawful actions in arresting an organization that had been known to hold subversive elements. When you are arresting someone, seizing their property, freezing their bank accounts and imprisoning those you catch is standard procedure. Those who resisted, did so until they had to be killed. THAT is something that can happen when you resist arrest with violence. The harder you resist, the higher the chance you will get killed. There will be an investigation into the Sunreavers and that's best done where they can be held in a secure place. You do not EVER leave a subversive organization intact or it will come to back to bite you in the butt.
As for due process, we, in this world, in the first world nations do not do mass arrests without due process. But Azeroth has no such thing. no nation of any faction or race has anything like due process. It's fully legal to do what Jaina did to a dangerous element.
I'm very well aware of the reasoning given to do all that, but at the end of the day, that doesn't mean it all didn't happen like Vyrin claims. On a large scale, no less. And mind you, the order wasn't to arrest the people who fought back, it was to kill
them. As far as I can see, it was a 100% chance that people resisting the arrest were dead.
In fact, its questionable why the Silver Covenant were enlisted to enforce this rule and not the Dalaran guards proper. We do see them hassling civilians Horde side as well. And please define to me what you mean by "subversive organization." If you mean the Sunreavers wholly supported the Horde and went behind the Kirin Tor's back to do so, I'm afraid that wouldn't be quite accurate. As it stands, its doubtful Jaina will conduct an investigation at all given her absolute certainty the Sunreavers are guilty, and her words during and after this incident.
"You are no longer welcome in Dalaran." "Your people are prisoners of war." "Once Horde, always Horde." Etc.
And the absence of due process is simply not true, trials and such does exist on Azeroth. Tirion Fordring was tried and found guilty in the book Blood and Honor