This probably isn't what you're looking for, but you can get the command prompt to start up minimized so that it's at least out of the way - which is what I do.

1) make a batch file to call perl and the program - put it anywhere you want.
2) make a shortcut to the batch file
3) in the properties of the shortcut, set the "Run" option to minimized. You can change the icon too. The prompt is still there, but out of the way. Maybe not the best method, but it doesn't take much effort.