Okay figured this out. If anyone figures this out without having to include the whole active list of values, please comment. The solution below will leave a recent system timestamp on all active values when new ones are inserted.
In a nutshell, use describe to get the Object, then Object Field Map, use that map to get the field to update, describe that field, get the Picklist values. If the picklist values are active, include them in the list to update.

 

webService static void updatePicklistField(String obj, String picklistToUpdate, String picklistLabel, String newPicklistValue)
    {

		//Get the details of the current picklist as we need to include the existing values
		SobjectType objType    = Schema.getGlobalDescribe().get(obj);
		Map<String,Schema.SObjectField> objFields = objType.getDescribe().fields.getMap();
		SObjectField fieldName = objFields.get(picklistToUpdate);
		Schema.DescribeFieldResult fieldResult = fieldName.getDescribe();
		fieldResult = fieldResult.getSObjectField().getDescribe();
		List<Schema.PicklistEntry> ple = fieldResult.getPicklistValues();

		MetadataService.MetadataPort service = createService();
        MetadataService.CustomField customField = new MetadataService.CustomField();
        customField.fullName = obj + '.' + picklistToUpdate; //This must in the format Object.Field
        customField.label = picklistLabel; //This field is needed in update
        customField.type_x = 'Picklist';
        metadataservice.Picklist pt = new metadataservice.Picklist();
        pt.sorted= false;
        metadataservice.PicklistValue newPlValue = new metadataservice.PicklistValue();
        newPlValue.fullName  = newPicklistValue; //This is the new picklist value
        newPlValue.default_x =false ;

		pt.picklistValues = new list<metadataservice.PicklistValue>();
		pt.picklistValues.add(newPlValue);

		//Add Existing values back in
		for (Schema.PicklistEntry pl : ple){
			if (pl.isActive()){
				metadataservice.PicklistValue existingPLValue = new metadataservice.PicklistValue();
				existingPLValue.fullName  = pl.getValue();
				existingPLValue.default_x = pl.isDefaultValue();
				pt.picklistValues.add(existingPLValue);
			}
		}

        customField.picklist = pt ;
        List<MetadataService.SaveResult> results =
            service.updateMetadata(
                new MetadataService.Metadata[] { customField });
        handleSaveResults(results[0]);
    }