1. Arrest (someone) for a crime.
2. Understand or perceive.
As with any "educated" vocabulary (in any language), using "apprehend" instead of "understand" in casual conversation may be considered erudite by some, but pretentious by others. You have to know your audience, and where it sounds appropriate. However it's not uncommon to see it written in articles, literature, essays, academic journals, and similar media.
That being said, I personally think this use in the example in your book is awkward. While "apprehend" can mean "perceive", the government isn't just noticing the social disharmony. It would be more natural to say that the government is expecting and avoiding social disharmony by preemptively banning these two, e.g.:
Anticipating social and communal disharmony, the government banned ...
or, alternately, that they are defusing the situation by banning the people they consider responsible:
Responding to social and communal disharmony, the government banned ...
There are many other ways to describe the situation, but I would be unlikely to use "apprehending" to do so.
Side note: "Comprehend" is a synonym for "understand" that (as Nic Hartley says) is slightly more educated but still very common. Again, it's not a word I would use in this context, but it's a lot less fancy than "apprehend".