Yes, obviously religious organizations can be immoral--because sin exists. You're still avoiding my question, why is this so difficult for you? Here, I'll copy/paste it for you again.
If people(you and I) decide what an immoral act is, then it's only a matter of opinion and no opinion on this matter is more or less correct. If I decide that murdering you and your family because of the color of your skin is moral, I'm just as correct as you are when you claim that is in fact immoral. Is that what you're saying? If not, then you have to explain what morality is and how moral judgements could possibly be weighed against one another.
Religion uses outdated black and white often arbitrary morality to solve decisions making. It works because its simple and simple minded can't think so religion becomes attractive option for them. They can outsource all their brain power into it.
Sin is a transgression against moral laws of supposed gods (in reality its people doing all the writing under false pretense)
You asked me how moral judgements could possibly be weighed against one another
Morality is a muddy concept. While generally very broadly
I agree that morality is subjective it doesn’t really address the nuance of all decisions. Its is like an on/off switch either right/wrong there is no in-between. Instead what you need is a thermostat. You might think that killing people because of skin color is right but a more accurate/effective way of doing it would be to employ a decision making on what works and what doesn't depending on where you are going or what you are trying to achieve. Its very convenient to blame a race or color of someone's skin it is very lazy thinking and might not be what you actually want. (Inb4 I activate sirlom's trigger word).
In a system of what works and what doesn't actions are judged solely on their functional outcomes not some absolute moral laws. Instead of right and wrong it becomes either functional or dysfunctional.