There have always been ideological differences within the Liberal party. In days gone by, they have always been held at bay by the greater lust for power. In recent times that balance has been precarious. Early on the exodus of Bernadi suggested all was not well. The issue of marriage equality has been a catalyst for great angst for the Liberal party going all the way back to 2004. When Howard altered the marriage act to stymie same-sex marriage.
We all know that some people within this government have strong religious beliefs that conflict with marriage equality. Religion & politics can coexist but they should be kept separate. This is great in theory but doesn't work in practice in my opinion. Being raised a Catholic until 18 when I walked away I can see how difficult it would be for somebody committed to their religion to be objective on issues that conflict.
The extreme right of the party wants religious protections attached to the marriage equality bill. Depending on who is delivering them they range from bigoted to just plain offensive to most people. They would also probably conflict with the Australian constitution s116.