Hi Christy!
First of all, yes, it’s true that amiina originally comes from Arabic. But I wouldn’t necessarily say that the word isn’t Bambara/Manding just because it can be traced back to that language.
Pinning down what words are authentically part of a language is a slippery slope. If you step back far enough, you can argue that almost any word is loanword from another existing or dead language. “Amen”, for instance, is arguably “not English” since it is originally Hebrew.
All of that to say that I would generally tell someone that “amen” is said amiina in Bambara/Manding because that’s what one generally hears people say.
But if I was looking for an alternative, I might use the following which one sometimes hears and reads in N’ko circles:
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Ala ka à kɛ ten
‘May God make it thus’
In Sulemaana Kantè’s French-N’ko dictionary he also lists another option which I say seen once or twice in texts:
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Nbàrin
‘Amen’
The first option, of course, is transparent to anyone who speaks Bambara. The second one, I am not sure.