No, it doesn't come from that.
I know, from personal knowledge, that the meaning can be something like "be it so/in truth/so be it", and this is confirmed in Wikipedia and also in the link below about pronunciation.
About the pronunciation, the OALD says that you can use either, apparently. The "syllabation/spelling" might just be a matter of "rhythm".
While, about the origin, the NOAD states:
ORIGIN - Old English , from ecclesiastical Latin, from Greek amēn, from Hebrew ' āmēn ‘truth, certainty,’ used adverbially as expression of agreement or consent, and adopted in the Septuagint as a solemn expression of belief or affirmation.