I just found out my commander is a government contractor. Can someone explain this to me?

Why do you think they just "made any civilian an officer"? Do you think someone waved a magic wand and put Captain's bars on a person and said "now you are a company commander"? Do you have any reason to believe the commander didn't go through a commissioning program and training? Many reserve units have non full time people as company commanders. It's a reserve unit, that's the point of them.

As stated very few units have full time commanders, most of the AGR's are usually NCO's at the company level, the training NCO, Operations NCO, Supply NCO, and if you have a maintenance platoon that is usually an AGR slot. Officers in AGR slots usually start at the battalion level or higher, every once in a while there is a commander slot that is AGR and the only reason for that is so AGR's can get command time. Out side of that every one is a citizen soldier.

Federal Employee here, but one of the most significant things you get while enlisted is a security clearance. And it is not uncommon for people to double dip as it is sometimes called, to be in the reserves while in some form of federal service.

On a pragmatic level of it, many civilian jobs have a lukewarm at best track record when it comes to maintaining reservist positions when they are deployed ( although keep in mind, just because something is illegal, that does not mean there is someone to enforce the law). And federal contractors and federal service both have very good track records for making sure that when you return that there is a place for you, maybe not always the same place you left, but you will return to a paycheck.