I know of another company that's been using Marketo for year to do this exact same thing (though their numbers are number higher). And unfortunately there is no automated way to do this.
Here is a related idea you should vote for:
Random sample to a fixed number of records
https://community.marketo.com/MarketoIdeaDetail?id=08750000000HaClAAK
And here another one - that should be merged with the first:
Cap Affected Number of Leads
https://community.marketo.com/MarketoIdeaDetail?id=08750000000JXZtAAO