As an aside, I would start both sentences with It is so,.
Something that is meant to be a certain way certainly indicates a purpose on the side of an agent that supposedly made it so.
Something that is supposed to be a certain way indicates a certain expectation from the side of the observer.
His artwork is meant to be shocking.
The artist has the intention to shock.
His artwork is supposed to be shocking.
Well, I heard that he meant to shock people with his art, but honestly, I do not find it shocking at all.
However, supposed can also mean that something is expected to be a certain way because it is the proper way for things to be:
The bus was supposed to arrive at three.
Are those holes supposed to be there?
Aren't you supposed to be at school?
Sometimes we can actually substitute meant in those cases:
Did you mean to make those holes there? (Or was it an accident?)
However, more commonly you would use should as a substitution:
The bus should have arrived at three.
Should those holes be there?
Shouldn't you be at school?
In your example, I would use meant.
Using the first sense of supposed, it was always supposed to be so seems like a rather non-committal ah well, we always expected it to be so, which can hardly be an explanation of why it is so.
Using the second meaning, it was always supposed to be so seems to indicate that in the past this was how things should be - but no longer. So again, it doesn't explain why it is so at present. If you change it to the present tense, you can get the desired meaning:
It is so, because it is supposed to be so.