OK, now I am sure that this does not always work. I subverted an army next to a city and it still came on to reinforce the garrison. This leads me to think that my previous observation of the same phenomenon was not in error. I am not sure why sometimes subverting an army stops it joining it's allies and sometimes it does not, but my experience is that it is erratic. Best to get the stealthy/night fighter trait to be sure, I reckon.