There's abstraction confusion here, though. All SQL injection countermeasures and all it would take to protect the above CLI call is respecting the actual language you're using. That is, not gluing a query/command from strings.

Starting a subprocess via shell is could in particular be solved by a simple API of the form of:

  system('yourapp', ['option1', {'option2' : 'something'}]);

in your favourite language. Handling pipes and redirects gets more complex, but I see no prima facie reason why it couldn't look like this:

  pipe(system('yourapp', ['option1', {'option2' : 'something'}]),
       system('grep', ['n', 'i', 'foobar']),
       system('somethingelse', [], null, file("/dev/null")));