All the tools you mention assume at their basis that you are developing a Worklight-based Hybrid application. So no, you cannot create a pure web app in Worklight, w/out the added Worklight-generated files. The build tool, the testing tool, the optimization tools, all work on Worklight-based apps.
Also, it's not that Worklight Server specifically costs money, Worklight costs money... you may not publish a Worklight application (either B2C or B2E) w/out a license.
You can evaluate Worklight by using the Developer Edition that you download from Eclipse Marketplace, but at the end you must purchase a license if you intend on going public.