Hi,
I see you have been online very recently.
I have been looking at the 1864 witness named as Elizabeth Macdonald, to try to confirm your thoughts that she may be the wife of the CofE minister. I find that the following live link that leads through to the lists of CofE ministers in Australia is very useful.
http://anglicanhistory.org/aus/cci/ . There is no listing for Aug Macdonald, nor an Angus Macdonald, nor as Mcdonald.
But, that led me to both the Vic BDM index and to Trove newspapers, including the Hamilton Spectator.
At Vic BDMs index there’s a number for births with parents as Elizabeth COGHILL and Angus MCDONALD and MACDONALD, babies born Hamilton, in the 1860s. – to me that confirms it is likely that where an Elizabeth Macdonald was recorded as a witness to a marriage in Hamilton conducted by Rev Macdonald that she could well be his wife.
So I continued to search for Rev Macdonald and my long held understanding that he was a Presbyterian minister.
I have found him via Trove. He was the Hamilton Presbyterian minister, and he was well regarded, and in 1868 he met a tragic accident leaving his widow, Elizabeth to raise their young family. Here is an obituary
https://trove.nla.gov.au/newspaper/article/194476231 Hamilton Spectator, 25 March 1868.
JM