What is the update / insert ratio? When there are not that much updates and a lot of inserts and there is a primary key you can use the solution discribed in the help of the insert/update step.
Insert - Update - Pentaho Data Integration - Pentaho Wiki
Note: Due to the extra lookup this step performs slower then a normal Table Output step. Another option is to use the Table Output step with error handling what is described in the chapter Step Error Handling. "If you put a primary key on the ID (in this case the customer ID) the insert into the table causes an error. Because of the error handling you can pass the rows in error to the update step. Preliminary tests have shown this strategy of performing upserts to be three times faster in some situations (with a low updates to inserts ratio)."