There's a difference between asking people to do something and asking them to do nothing though. In general, bodily autonomy is important and this the best abortion defense in my opinion as an anti abortionist.
While there is a difference, bodily autonomy is about the right to make decision around your own body, not the right for your body to run on it's own. So I would argue it is not a good argument as you say.
But your body runs according to the dictates of nature, not solely your will.
For example, my body often breathes even when I don't particularly will it. I also cannot stop the process of digestion with my mind. If I were to ask for the 'right' to stop digestion by asking a doctor to sever my intestines, it would be good for the government to then charge such an irreputable doctor with assault and maybe murder.