Hear the Code to remove the Product Based on SKU
Request Example SOAP V1
$client = new SoapClient('http://magentohost/api/soap/?wsdl');
// If somestuff requires api authentification,
// then get a session token
$session = $client->login('apiUser', 'apiKey');
$result = $client->call($session, 'catalog_product.delete', '1');
var_dump($result);
// If you don't need the session anymore
//$client->endSession($session);
Request Example SOAP V2
$proxy = new SoapClient('http://magentohost/api/v2_soap/?wsdl'); // TODO : change url
$sessionId = $proxy->login('apiUser', 'apiKey'); // TODO : change login and pwd if necessary
$result = $proxy->catalogProductDelete($sessionId, '6');
var_dump($result);
Please see the Image for Request and Response Data
For More Reference Please Check This Link.
Best Answer
Did you try an import module like FastSimpleImport?
I haven't tried, but it seems to support configurable products. It is free and opensource, you should give it a try.