How to talk to my civilian employer about their constant need to assume I have underlining issues due to my service?

My feelings on this will be unpopular, but they are based on fifteen years of objective thinking about the subject.

Yes, you have certain rights to protect you. That does not change the fact that your decision to not only hold two jobs instead of one, but also to make the side job (NG) your higher priority, does make you a liability to other team members in terms of how much they can depend on your availability. Everything in that statement is a mathematical fact, not an opinion. So I can understand some amount of frustration and resentment.

That does not by itself make you a poor employee or detrimental to your team; I do not know you and am disinterested in making personal judgements anyway. Nor is it my business why you chose to split jobs instead of choosing one to dedicate towards and excel in. But you yourself opened by saying you hold a senior position in a company with little personnel but significant revenue. Your profile says director of operations in a construction franchise. I expect that position requires work and real time communication that falls outside neat schedule blocks, and I have the feeling you lack the personnel to cover down when you are unavailable (unless the fill in person is the owner, and I know I would not like to have to keep bothering the owner because my contemporary is often unavailable- it would make me look weak myself). I also imagine that the people who were informed in your interview that you had this higher-priority side job and hired you anyway aren't really the ones who have a problem with this.

It also sounds like there is either a personality conflict (your way of doing things) or resentment of your side job, and that fuels the antagonism. That may be completely unreasonable for the other party to do, but that is life.

As I said, I am not taking any stance on who is to blame. I am giving you the respect of an honest response to exactly what you communicated. The only safe solution I can think of without more information is perhaps considering how this person (if it is just one) differs from you in terms of personality. I do not know how much academic leadership education you possess, but my best advice is to find a different way to communicate and work together. Last year I listened to a series of short audiobooks by Clayton Geoffreys, each one focused on "Understanding & Relating with the [Logician, Leader, Inventor, etc.]". It is essentially about working with different personality types. I found it helpful for increasing productivity and efficiency through lowering conflict and miscommunication with different types of people. I think we BADLY struggle with this, as Soldiers and as Sappers; our culture is very unusual. It might also be wise for you to speak to some practicing engineers in your unit, asking them how they deal with what you are going through (I am certain real engineers who are also working two jobs have often run into these conflicts).

EDIT: One final note. There is the possibility he is simply confused why you don't do Army full time if it means so much to you. Clearly he does not have a real complication of all the roles of the Guard, and while I never would have chosen anything but Active for myself (again, I am not trying to get you to explain your reasons for your career choice), I would not be surprised to learn that a 12B unit is among the most useful and utilized in the Guard due to versatility in non-combat operations, both statewide and abroad. Perhaps that coworker does not understand anything about the Army beyond infantry and tanks, or the Guard as anything but part-time and local; in other words, maybe ask to go to lunch together or for beers and provide a well-planned/composed five or ten minute explanation on how this works, what you do, and why you chose to do what you do the way you do.