It is the same with your conscience. You can only follow it on matters that they say are OK. So in the days when alternative service was a no no, anyone whose conscience allowed them to do it, instead had to abandon their families and serve a prison sentence instead, even if that action went against their conscience.
I have always found it amusing that the WT must have a view on almost everything, and dubs must conform, even when the issue has no bearing at this time. A prime example of this is, “will those destroyed at Sodom and Gomorrah be resurrected?” Even though the answer to that question has depended on what year in which you ask it, dubs must fall in line with the prevailing view. I once asked a dub that called on me, “Why does the WT have a view at all? Why don’t they just say, ‘we don’t know’? We don’t need to know.” His answer was, “we are a united people and we must have unity”. So sad really.