The Transform Data Task Properties - Option tab allows you to specify "Max error count" which is supposed to allow the package to keep going until the maximum is reached. If you know about how many duplicates you have, you can experiment with this number. Given the unpredictability of data, I've not had good luck doing this, but sometimes it comes in handy, and you were looking for some alternatives. Also on this tab is where you can specify the exceptions file for the bad data.