By default, the kphp command makes a binary launching as an HTTP server.
To compile just a console PHP script, use
-M cli option — while compilation (not while execution):
kphp -M cli [...all other options] index.php
Just executes your script and exits.
Lots of server command-line options are just skipped in this case.
Console arguments, argv
You can use $argc / $argv superglobals in a PHP script. To pass them from the console, use
./kphp_out/cli arg1 arg2
Then $argv will be
[ 0 => "/path/to/kphp_out/cli", 1 => "arg1", 2 => "arg2" ]
$_SERVER[‘argv'] will be the same — as in PHP.