Well let's see. Shinra was basically taking on the role of the government (or governing the city). And lots of people are controlled by their government like that (or have been in the past).
And all they were doing was trying to find out things about a person who they deemed as the bad guy or one of the bad guys. Compared to in Xenogears where they have 13 year old girls piloting superhuman gears that nobody in the world can pilot.