The reason that developers are abandoning, JSP, ASP, PHP for JavaScript apps is because the benefits far outweigh the drawbacks and those benefits would still exist even if JavaScript was double the cost per line (which is the worst way to measure the cost of development).
JavaScript allows us to reduce the technology stack from a bunch of proprietary server languages that are not portable among server, to the browser which is very portable. When a JavaScript front end is designed to communicate with a REST facade, it makes the front end portable among any of the back end choices, further it provides a way to allow a front end to utilize completely disparaenent back ends (think Facebook and twitter integration).
JavaScript forces you to look at your business as a set of services forcing you to develop a service based platform. The advantages of this are becoming more and more apparent.
Finally, in forcing the service based architecture it becomes easy for companies to rapidly produce front ends for platforms like the iPhone or IVR. Delivering to new platforms becomes a rapid development exercise because JavaScript web apps inherently force you to decouple the UI from the business systems.
There are a lot of advantages to developing applications with JavaScript few of them have to do with the cost of line by line code and more to do with total cost of ownership and technical debt. When those are factored in the value of JavaScript apps becomes apparent.
I use Netbeans, it does not get a lot of press but they have been outpacing many of the dedicated JavaScript IDE's they have great JavaScript support.
how do you rename a method for example with the tool use (imagine that another method with the same name exists in a different class/module)
I use Dojo for large JavaScript projects, there really is not an alternative when you get the the application sizes I deal in, as such everything is namespaced. Netbeans can refactor methods in JavaScript, so I use the built in functionality of the IDE to do so.
These tools exist. Emacs, Vim, Komodo Edit/IDE, ... Visual Studio might even have support for Javascript at this point.