Can I use Aprobe to change the command run by a call to system() from my application to run my own little script instead?

Yes, replace the parameter to system() with a path to your script. Imagine the possibilities.

For example, here is a small C program that calls system():

#include <stdlib.h>
main()
{
  system( "/bin/ls -al" );
}

Here is my_ls.apc, which is a probe that you can apply to the program:

// change these 2 lines to work on
// a different command:
static char cmd_to_change[] = "/bin/ls";
static char my_script[]     = "/tmp/my_ls ";

probe thread
{
  // it's in "libc.so" for Solaris
  // it's in "libc.a(shr.o)" for AIX
  //
  probe "system()" in "libc.so"
  {
    ap_NameT new_command = NULL;

    on_entry   /* to system()" */
    {
      char *command = (char *)$1;

      // for debugging, let's give some
      // info about where we are:
      log( "system() called with ",
           ap_StringValue($1));
      ap_LogTraceback(99);

      // make sure we only replace
      // the correct command
      {
        char *cmdpos =
           strstr(command, cmd_to_change);
        if (cmdpos == command)
        {
          // replace it, but preserve args
          char *argstring =
             command + strlen(cmd_to_change);
          // allocate and build a new_command
          new_command =
             ap_CatenateStrings(my_script,
                                argstring,
                                NULL);
          // this replaces it:
          $1 = (int)new_command;

          log("*** changed to: ",
              ap_StringValue($1));
        }
      }
    } /* on entry */

    on_exit   /* from system()" */
    {
      // indicate the return code for the
      // system command:
      log("system() returns ", $0);

      // free our string:
      ap_StrFree(new_command);
    }
  }
} /* probe thread */

Here is the contents my little script /tmp/my_ls:

echo "MY_LS: --->"
ls -ltF
echo "<---- MY_LS"