I want to use some variables in a geoprocessing service like a URL, that should be configurable from the arcgis ardmin or manager. Is it possible have a tool input, which value will be specified by the admin, after the service have been published?
I usually recommend doing that in this way.
Create a skeleton Python file which you will turn into a Python script tool in a toolbox.
sys.path.appendto append the folder where all the "meat" .py files will be stored.
Then just import those files as modules. Place a configuration file (can be .py or any other file) there.
This will make it significantly easier to modify the code since you won't need to republish the service (or manually update the published code).