My interpretation is that with the SAR you're identifying illegal activity, and the funds from the sale of marijuana would be considered illegal. If you don't believe that the other funds they've deposited into the account are illegal then I think you'd be justified in not reporting them, but I'd document why those transactions are not suspicious clearly for examiners.
We do not bank direct MRBs, so when they do open accounts with us it's generally because they've misrepresented their business purpose during account opening. For that reason, we'll file regardless of what the source of funds may have been, so for my purposes I usually consider the clock ticking as soon as we learn of it.
Daisy's question is key, if it's at all ambiguous in your policy whether you allow these businesses, and if so under what circumstances and with what due diligence and SAR controls in place, I'd make writing all those P&P first priority. There's probably lots of good reasons to bank these businesses ($$$), but I'd personally be nervous to start during the same year that CDD became a pillar and the Cole Memo was rescinded.