For adding new attribute values it is better to use the value**s** key in the option array. This is expects entries with key `sortOrder` and value `label`, while the approach you are using expects the optionId as key.

Change your code like this:

	$attribute = $this->_eavConfig->getAttribute('catalog_product', $code); 
	$attributeId = $attribute->getAttributeId();

	$option = array();
	$i=1; //sortOrder counter

	$option['attribute_id'] = $attributeId;
	//use the 'values' key to add new option values; that array contains the sort_order as key and the label as value
	$option['values'][$i++] = 'value1';
	$option['values'][$i++] = 'value2';
	//...
	$this->_eavSetup->addAttributeOption($option);

For better understanding of what'S happening there you can check the method `addAttributeOption($option)` in `Magento\Eav\Setup\EavSetup`.

I hope that helps. Feedback would be nice.