Pentaho Data Integration (PDI, aka Kettle), comes with a command line tool called "kitchen" which you can use to run .kjb files. (FYI, "spoon" can be used to run .ktr files.)
You can use something like the shell_exec command in PHP to run your .kjb file using kitchen, just like you would run it on the command line.
If I remember correctly, you need to make your current working directory be the directory that the kitchen.bat (or .sh) is in before you run it - I don't remember why, just that we had to be in that directory for things to function properly.