Yes. If you open the scriptcraft.jar, you'll see that there is a boot.js file in there. However, like adding code into any other plugin it's probably not a good idea to do injection like this. ScriptCraftJS already has the plugins folder for exactly this purpose. From the doc:
At server startup the ScriptCraft Java plugin is loaded and begins automatically
loading and executing all of the modules (javascript files with the extension .js)
it finds in the scriptcraft/plugins directory".
Any help?