There's very little that I disagree with here. I agree with the second part, and I agree with most of the first part.
I don't see that it implies autonomy (from the brain and its activities). I accept that I cannot make decisions without a brain. A brain's function enables me to make decisions. What you suggest is that we are our brains. We are more than that.
The way you phrase it does appear to imply some degree of autonomy for conscious self. Your comment, for example - ''a brain's function enables me to make decisions'' appears to delineates 'me' and 'a brains function' in the sense that 'a brains function' enables 'me' to 'make decisions' - as if the brain and its activity is a means for 'me' to make decisions rather than it simply being the brain that makes decisions in the conscious form of 'me' making decisions....if you can see that distinction.
I see the distinction, and when they bury me, they'll bury more than a nonfunctioning brain. Recall, I am more than a functioning brain. When I'm dead, I'm more than a nonfunctioning brain.
Further:
A functioning brain is required for me to have a mind, but if I'm brain dead, there is no mind, and without a mind, the essential part of me that makes me, me, is gone, but when they bury my body, they are burying me, the body (and a nonfunctioning brain), but no mind is buried.
The part of me that is neither the body nor the brain itself (but rather something that is a consequence of a functioning brain), the mind is more palatable as something that can be said to make decisions. Even still, there are phrases like "I made up my mind" too, that have this seeming implication you speak of.
I'm open minded to people of science teaching us things, but when they do, I try to incorporate their teachings without forsaking how normal people speak. Language is ... important. It's not always that what we say is incorrect; the problem is that when new things are learned, we are often told that we were mistaken about what we thought, but that's not always it--and when language gets twisted along the way, a defense of a way of speaking can unfortunately give the appearance of denying what science teaches.
I've always said that it's not the science that is the problem. The experiments, methodology, the whole shootin' match, all fine. It's the scientists that is at issue. They do great too, until they get to the very end and interpret their results using words.
Philosophy has produced people that have come to say the darndest things, and I gotta tell ya, scientists do a wonderful job as they keep us on the forefront of new knowledge, but when it comes to speak of their wonderful scientific findings, the philosopher inside them bubbles to the surface when they stop doing what they do and start telling us the implications of what they have found.