There is now a way to Rollup a unique count of records, natively in Rollup Helper!
The option to do so will be available when you are creating a count Rollup, in step 3 of the Rollup Creation Process.
After you select your Rollup Type of Count, You will want to check the 2 boxes: Change Source Field Unique Count
The field you want to be unique will be the field that you set as the source field for the setting.
It will then count the number of different values stored in that field, instead of just counting all records! You can set the source field to be a text field, or any other field on the source object you are rolling up from.