a batchfile will use START "Name" "PathtoExtendScript" "PathToJsxBin"; so it'll have to launch ExtendScript.
As a alternative you can launch the jsxbin by a vbscript or vbscriptexecutable (exe, just export the vbs as exe ...)
Set fs = CreateObject("Scripting.FileSystemObject")
Set js = fs.GetFile("c:\HelloWorld.jsxbin")
Set myInDesign = CreateObject("InDesign.Application.cs5.5")
myInDesign.DoScript js, 1246973031
Edit: To export a vbs to exe use for example: