Why not just call your Autoit / Autohotkey script from your C # program using the System.Diagnostics.Process class?
ProcessStartInfo psi = new ProcessStartInfo("your_script.ahk");
psi.CreateNoWindow = true;
Process procScript = Process.Start(psi);
procScript.WaitForExit();
CreateNoWindow = true, , , WaitForExit(), .
AutoIt AutoHotkey , . #/. NET, , , .