At issue here is how we treat one another. The foundational theological concept here is that of human beings as bearing 'the image of God'. From that follows the understanding that there is a special dignity and value in human beings that must be respected and honoured.
I think this is what the 90 day limitation threatens to deny. To lose employment without warning or reason and without any opportunity to defend oneself is an affront to basic human dignity. When someone enters a workplace they not only bring their labour, but they also enter into a social domain of relationships and give something of themselves. While any dismissal severs those relationships and potentially devalues the person, to dismiss without any reason is an affront to the dignity and value of the person who has been in that place, even if only for 90 days. We owe each other something better than that.
At stake here, is what it means to be human. The Government seems to be losing sight of that.