To delete a ScormPackage from the SCORM Engine system (database only), you can use the ScormEngineManager.DeletePackage function. Here is some example code to do this in c#.
// Replace 'Vanilla' with your custom Integration Class
VanillaExternalPackageId pkg = new VanillaExternalPackageId();
pkg.ParseFromString("CourseId|123"); //use your custom package keys here
pkg.VersionId = 0; //or whatever specific version you want to delete
VanillaExternalConfiguration externalConfig = new VanillaExternalConfiguration();
externalConfig.ParseFromString("ConfigValue|abc"); //add your config string if applicable
//Now delete the package
ScormEngineManager.DeletePackage(pkg, externalConfig, Scope.SPECIFIED_ON_EXTERNAL_ID);
Notice that you are setting the specific VersionId (defaults to 0 so if you only have one version, use 0) and the 'Scope' is set to SPECIFIED_ON_EXTERNAL_ID.