During Hetherwick's later years in Blantyre he was not only Head of the Mission but increasingly had a significant role as a church leader. He had seen the early beginnings of what would become the Blantyre Synod of the Church of Central Africa Presbyterian (CCAP) but at first it was a matter of just a few dozen who had been baptised. By the turn of the century, it was a few hundred and by 1914 had increased to 11,630. In the organisation and development of this emerging church community Hetherwick had a leading role to play. At the same time, he was much occupied with the question of how this young church would be related to the other churches that were emerging in other parts of the Protectorate, particularly those originating from the Livingstonia Mission in the north and the Dutch Reformed Church Mission in the central part of the country. What sort of connection these might have with one another and what kind of church might result from their interaction were questions that loomed large in his mind from the early 1900s onwards.

For his final sixteen years, from 1912 to 1928, Hetherwick lived alone in Blantyre. When he and Elizabeth went on furlough in 1911, they took the decision that Elizabeth and the children, Clement and May, would remain in Scotland while Alexander returned to Blantyre by himself. It was a common dilemma in those days for missionary families – they wanted their children to have the opportunity to be educated in their homeland and either had to leave them in the care of relatives or the mother had to remain at home while the father continued his service overseas. The dilemma was particularly acute for the Hetherwicks, as Alexander later explained to a colleague, ‘I think the holiday time is more important for the girls than the school time. It was holiday time that made Mrs Hetherwick stay at home with May – had we had anyone to take her for the holidays it would have been different – but neither of us have any relations and one does not like to entrust one's girl at a most impressionable age with strangers.’