did you consider using the policy assigment rules? These might be just for the purpose you mention here, I think. You create a policy assigment rule for all your SQL server another for all your Exchange servers. First rule have the policy with exclusions for SQL servers the second with exclusions for Exchange.
You need to apply tags your particular servers for this and assign the respecitve policy rule to those tags (the policy will be applied to systems that have those tags). All you need to make sure that your tags are applied to each new server that are created.
See also ePO 4.6 manual p. 166.
Otherwise what prevents you from applying the exclusions in the general policy? You can say that those exclusions will be never met in the case of non-SQL and non-Exchange servers, and according to my (previous) information, around 1000 exclusions will there be a noticeable lag in OAS scanning.. Just being curious...