How can I prevent Pentaho DI/Spoon from deadlocking?
Noob error!  Pentaho "hops" are not sequential; they will all run simultaneously.

The correct way to handle this type of process - read data, write data, and then manipulate the data in SQL - is to put the read/write in a transformation by itself, and then put that transformation into a job with the SQL procedure(s) following the transformation.