I'll ask again, is there a reason why you need to use a Script component as your source to read from a flat file? It sounds to me like you're adding in a level of complexity when you could just use the flat file source adapter.

As far as your error goes, create an OnError Event Handler and set the Propogate system variable to false in the Event Handler. This will prevent an error from bubbling up and erroring out your for each loop. Instead of failing the for each object, it will just stop execution of that iteration and begin at the beginning of the for each with the next iteration.