The new version of the toolkit allows you to deploy individual web resources which is fantastic.
If I write click on the CRM Package project, select Deploy and chose an individual web resource, then it seems as if all that happens is that the web resource gets deployed.
If you right-click on an individual javascript file within the project and select deploy this kicks off a project build, and seems to try and deploy database projects which are present in the solution, before deploying the javascript web resource.