Hi ChanKK,
I believe you will need to create a Pre-Post Deploy Script to take care of that situation. Keep in mind that you can use the Priority field to control which script or functionality to run first. You can create the scripts to drop the PK constraint in SQL Server Management Studio (SMS) then copy them to the DDT Pre-Deploy script.
Here is a sample of what I have in one of my DDT Post-Deploy Script:
/****** Object: Index [DuplicateImportCheck_idx] Script Date: 04/07/2010 09:50:41 ******/
IF EXISTS (SELECT * FROM sys.indexes WHERE object_id = OBJECT_ID(N'[dbo].[TransactionItemsImport]') AND name = N'DuplicateImportCheck_idx')
DROP INDEX [DuplicateImportCheck_idx] ON [dbo].[TransactionItemsImport] WITH ( ONLINE = OFF )
PS
When copying the script from the SMS do not use the command "GO" or "USE database" since it will give you an error in the DDT when trying to deploy your package.