If a college doesn't like seeing the R&S levels on the transcript for high school, I personally would just leave it off. You are finishing a more than full and complete English program each year. For example, you are completing all of BJU English along with a writing program for the WG guide along with some R&S. That is MORE than enough English to be counted for credit IMHO. Plus - I honestly don't even remember having "grammar" in high school at all. So I would think that you could include it or not and your transcript would still be plenty full.
I am sorry to read that your state has such low scores and that people don't trust in homeschooling much there. That definitely puts you into a difficult pickle. I am not sure what your child's goals are when he finishes high school but your son could always take the GED if you were concerned. My husband and his brothers were both homeschooled and gradated between a span of 12-18 years ago. My husband went to college with no diploma and no GED. Both of my brother in laws had to get their GED though. My husband went to college straight out of high school. My one BIL started a couple of years ago but it was 10 years after high school. My other BIL never went to college and he needed a GED for the job he has now. I live in Ohio and I guess it really depends on the program and school. I am going to push my kids to go to college straight out of school. If they need a GED to get into college, that is fine

I don't really care

I figure they will have an absolutely fantastic education and should have no trouble with the test. However, I do know that most local universities in proximity to where I live are very homeschool graduate friendly especially to kids that go to college right out of high school.
Sounds like you are already praying about it

I think that if you do decide to try out HOD next year, that will probably help in guiding you on your path tremendously. For us, this is a perfect fit. There is pretty much no way I would ever consider switching. But you would need to decide that for yourself. There is nothing better than finding a great fit for you and your kiddo. And if this did turn out to be just right, God will be with you every step of the way through high school and beyond.