This is really a matter of bank policy. Technically, the business IS the individual on a DBA, so there would not be any regulatory issues with giving cash back of which I am aware.
However, I do not think it is a good idea operationally. You put your tellers in a position where they need to make a distinction between DBAs/Partnerships/Orgs/Corporations when deciding whether cash back is allowable. I think the safest thing to do would be to require deposit of the full check if it is made out the the business and let the customer withdraw the amount they want back.
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Opinions are not necessarily those of my employer and should not be construed as legal advice.