HI Evelyn,
How do you flag customers currently in SFDC? I.E, if you're using SFDC Type is customer, then you would use that as a filter to take down their score. Dependent on how you segment customers from prospects, you will use that criteria to set up and reset and/or decay scoring campaign to prevent them from qualifying for MSI. Also keep in mind that leads that show up in MSI depends greatly on your overall scoring methodology as well as how many leads you have that are scored against each other.
The simple answer is create a smart campaign based on their qualifying criteria as customer and in the flow step reset or decay their score. I recommend using scoring tokens if possible to keep your scoring program manageable and consistent.