When typing this command line on windows : "pathToAnimate.exe" "pathToScript.jsfl" [-AlwaysRunJSFL] it still open the dialog box. Based on this documentation :
"'flash.exe' myTestFile.jsfl [-AlwaysRunJSFL]
Use the -AlwaysRunJSFL option to bypass the dialog box that prompts you to confirm script execution"
it should only execute the script without dialog box.
Thanks in advance for the help !