I would suggest to the user when he enters my system to create a site shortcut on his computer, this can be done manually by going to "Mais Ferramentas -> Adicionar a área de trabalho" :
How could I do this programmatically? is there any chrome api or native function that will allow?
Dude, if I were you, I'd make a file .bat and call it running with Javascript.
The Javascript file:
var objetoMan = new ActiveXObject("Scripting.FileSystemObject");
var WshShell = new ActiveXObject("WScript.Shell");
var oExec = WshShell.Exec("c:\temp\SeuArquivo.bat");
The file .bat :
copy \server\programa\NomeDoAtalho.lnk %userprofile%\desktop