It's quite normal for a refugee to wait for 2.5 years to get his/her case finalised and approved by the DIMMA (the department of Immigration and Citizenship). In some cases, refugees have to wait for 8-10 years until the government finalises its decision. I am not trying to scare you, it's not always a happy ending story with a refugee application. But there are heaps of people who made it.
1. If he already lodged in his refugee application visa, then you probably have to wait until it's approved then he can apply for another visa for you and your little one. Once he is granted a refugee visa, he will have the same right as a permanent resident visa holder does, who can sponsor relatives and families to come to Australia.
2. Any dependent children and partner can be included in the application for a refugee visa. I guess he has lodged it in already without including you and your baby. He probably won't risk it to start the process all over again.
3. As far as I know, his refugee status won't change if he marries you.
4. I am not sure what sort of documents will you need for a marriage in Indonesia. You have to find out whether it's possible for a refugee who has no passport or any identity cards to get married in Indonesia.
Here is the link to the Australian immigration website:
Maybe it's a good idea to talk to any lawyers dealing with refugees in Australia. Good luck!