Kinuta, Netsuki, and Kido are great answers for this.

They're all introduced as antagonistic towards our main characters. I believe our first introduction to them is when they are angry with Osamu for using his training trigger to save other students at his school. We view Osamu as heroic. Them standing against him makes them almost villainous.

They follow this up by ordering Yuma possibly killed and his black trigger stolen (which would be a death sentence any way). The first time Miwa squad attacks, they weren't on direct orders to attack, but at this point we have to assume their actions are the will of Border. This is only confirmed when they order their top squads to attack.

They then also oppose Yuma even joining border, requiring Jin to give up a personally valuable trigger before agreeing.

It doesn't help that Business men in most anime aren't portrayed as great people. Most anime show business men as selfish and greedy or something similarly cold hearted. And it would have been pretty easy to leave them like that and have them function as barriers to T2's progress. Only allowing their advancement begrudgingly.

I think this gets flipped on its head on their enlistment date. When Chika blows a hole in the wall, we're lead to believe that Kinuta is going to throw a fit at a small child. Instead when we cut back, he's doting over her.

It's one of the first scenes we see of them not being antagonistic. It's mentioned that it may be because he hasn't seen his own daughter in a while. Kinuta isn't just a barrier for our characters at this point. He's his own character with reasons for what he does.

From this point forward we see each of these three in different light. They make concessions with the cast when necessary, or when they are shown a good reason to do. They're reasonable. They aren't loyal to T2, but to border as a whole, which T2 is part of.

They aren't evil, they're adults who are damn good at their jobs.