You cannot hide the IDE in background during script execution.
However,there's an alternative to view the logs.
You can install the package which launches your sikuli via command prompt(sikuli-script.jar),
refer to https://launchpad.net/raiman/+download
you won't need the IDE to launch your scripts this way.
Now after changing necessary environment settings you can type-in simple path like "java -jar %Sikuli_Home%\sikuli-script.jar -r %Sikuli_Scripts%\main.sikuli" in cmd and get started.
here 'main' is my driver script where I have imported my modules under single .sikuli folder (main.sikuli) you can have any file name like abc.sikuli
(here you need to store your path in a variable like ,path = os.environ['Sikuli_Scripts'])
Also ,it is a good practice to launch applications creating batch files and accessing files using relative path.