Arabic in Course
I am only 15 or so lessons in, but my friends who are indo and watch me take the course from time to time always hate the use of Arabic words in the course. They tell me that yes Muslim people do use them, but it is typically used between them and other people. They would not use these words when speaking to you, and if you used these words when speaking to them they would assume you are uneducated in Indonesian, or that you are Muslim yourself. Creators of this course can you please try and keep this a neutral indonesian course and not bring religion into this.
Well, if you're watching Indonesian movies, you will hear "Assalamualaikum" at least once. You might not use it, but that doesn't hurt you. If you can get additional knowledge, why not?
This course is quite neutral, actually. Well, I don't know about bringing religion (I am secular personally) but telling people "Merry Christmas" or "Happy Eid Mubarak" is a custom in Indonesia, even though you might happen to be an atheist (I am). This is more of a representation of Indonesian society, however.
The Indonesian society is more into social solidarity, different from Western's value - liberalism. I guess that's a bit of cultural difference. Indonesians are used to care about minor stuffs like this. You'll be greeted "Merry Christmas" if you're a Christian.
I don't think it's a matter of bringing in religion. It's that those two Arabic greetings are commonly used in Indonesia - sure, you wouldn't be expected to use those words, but it's a part of the local scene y'know? They have religious origins, but they are often nowadays simply used as greetings or (unfortunately) catcalling. It's a part of the "learn about Indonesian greetings package". I think their usages in this course is perfectly neutral.
As a native Indonesian speaker and an ex-Catholic (now atheist), I disagree with what your friends said. It's not only used between Muslims; it's uncommon between two people where neither is Muslim, but not notably unusual. People also wouldn't assume you're uneducated if you use it in Indonesia as a visitor - they'll assume that you're trying to blend in with the locals and that you did your research.