Even if we grant both your points, then yes, those would still be civilians. Civilian =/= "good guy" or "innocent victim." It means they're not part of a military force.
Mind you, I'm not weighing in on whether or not the tactics here are appropriate, but it's pretty clear that the article is trying to make the argument that civilians are being caught up _military_ tactics which could eventually cross the line into strict war crime territory.
No. The ICE agents are presumably assuming that their victims are illegal immigrants, if we assume a best-case scenario where they aren't intentionally abusing their authority to attack random targets of their attention or racism.
But by legal definition, their targets are all innocent of crimes. Without due process, they are not convicted criminals.
Even if all this were true, your accusation would be false. Some came here legally, but in the eyes of the current administration violated the rules of their immigration while here.
One of the central principles of a democratic country is that the military is not used against civilians. "But those civilians are criminals" is the excuse that every president who wants to use the military internally will make. Civilians have rights, and if they're suspected of a crime, that's a matter for the police and the courts, not for the military. If you give the executive the power to send the military onto the streets, that is an extremely dangerous concentration of power in one person's hands.
The use of the military against civilians was one of the main grievances that led to the American Revolution (most notably, the British government sending the regular army into Boston to "restore order"). Many of the founders of the US were opposed to the idea of any standing army at all in peacetime, because of its potential use against the citizens of the country.
The military should never, ever be used to "police" their civilians. You could be forced to apprehend your relative. When the military attacks the civilian population then civil war is inevitable.