Couldn't you run a query similar to this:
listOfConflictObjectsInSystem = [SELECT Id,Field_A__c,Field_B__c FROM ObjectName n WHERE n.Field_A__c = :objectToAdd.Field_A__c AND n.Field_B__c = :objectToAdd.Field_B__c];
(sorry for formatting I could not find the salesforce code styling tags)
Checking the size of 'listOfConflictObjectsInSystem' will tell you if any objects are already in the system containing the data from those two fields. As long as these are uniquely identified.
If the combination of the two added together make it unique then create a formula field on the object that combines the two fields and query off of that field.
I have done this in a few of the systems - sending the list of objects in conflict to a visual force page and giving the user adding the record a page showing all the duplicates found for the object they want to add. I also add in functionality for this to be overridden in certain cases.
If you are trying to deduplicate the records already in the system than a data loader will need to be used - like sfdcfox already stated.