I don't think you are at that stage yet. You need to see those two death certificates to see what else they tell you before you start trying to look for Angus Kennedy's parents. For instance, was the Angus Kennedy who died in 1857 the father of your Donald/husband of Ann McIntyre? How old was he when he died? When did he emigrate to Australia?
There are many people whose baptisms are missing from the surviving records, so you cannot assume, just because there is only one possible candidate, that it is the right person.
How do you know that Charles and Cora Kennedy were the parents of Donald, aged 5? Does the passenger list specifically say so, or could Charles have been a brother or cousin of Angus, bringing Angus' family to join him once he had got himself settled in Australia? Have you found the deaths of Charles and Cora, and if so what do they tell you?