Being the author, you have the ultimate decision of whether or not to include magic into your novel. In your question, you said that the element of magic feels forced. Normally that would be a good indication that you should either change your approach, or remove it completely.
The central theme of your story sounds like it revolves around these government agents and their interactions with "special people". You would need to figure out what kinds of abilities these people have, and how the government can leverage them.
You would also need to answer the question why these people developed magical powers. What makes these specific people of millions, or billions of other people different than the rest? Is there some kind of special circumstance that occurs when people live in this specific area? You don't have to go into great detail explaining the process, but as the author, you should at least have an idea why. In fact, the less technical you can get with it, the better off you are because people who are very technical will have a tough time suspending their disbelief if you describe a process that would not be possible.
Magic seems to work quite well in small doses. If too many people have the power, or their power is too great, then these people may appear too much like a super hero, than a regular person. The best example of this is Superman. Sure he is super strong, fast, can fly, see through walls, etc. But, he is nearly impervious to all physical danger except for a rare element that is really no more than a MacGuffin. Most people really do not feel worried about Superman because he basically never loses. To balance this out, the characters with powers should remain mortal, and only have slight advantages over the rest.
If you do choose to include a magic element in your story, try to balance it out as best as you can. Magic cannot be the answer to everything, and if it is, then it becomes very cheap feeling.