Legal advised us not to go to the non-profit with our concerns.
Poor moral advice. Perhaps even worse legal advice. If he is embezzling and they ever figure it out, they will also figure it out that your bank knew or should have known. You have the deep pockets and they will want it to be someone else's fault.
I would be happy to testify for the charity about your bank's culpability, no charge.
As for filing a continuing SAR, the activity stopped; you have nothing to report. Regardless, your bank now has an excellent reason to sit down with the employee and ask why the cash deposits stopped.