I like the idea that a couple of people have posted about discussing first what the official plans of the church are should any type of violent encounter happen there, using whatever examples of other church violence you feel comfortable talking about. If the answer indicates that these issues have been discussed and that there is a plan to protect the congregation, the pastor may well be predisposed to grant you permission to carry.
On the other hand, if the answer gives you the impression that the pastor would not look favorably on you carrying, I'd confirm that MI law does not provide for any criminal charges should you carry to church without permission - i.e. that the most that could happen should you be discovered is that you could be kicked out of the church. If that is the case, then you have a decision to make:
1. Carry in some manner that will virtually guarantee you won't be made, so as to be able to protect yourself and your loved ones should the need arise. OR
2. Choose to be unarmed at church in order to not break the rules of both the church & the state.
I'm sure you want to do the "right thing" by asking your pastor (why else would you have posted your question otherwise, right?), but you have to ask yourself - is the "right thing" in this case to ensure the protection of yourself & your loved ones, or to follow the man-made rules of the state & the church?
I know what I'd choose, but the decision is obviously up to you and you alone. The fact that you asked for input tells me that you are thinking about the choice seriously, and that whatever decision you reach will be the right one for you. And that's all that really matters...