Try jsHybugger: http://www.jshybugger.org/
It lets you set breakpoints, singlestep, catch exceptions, and interact with the JS/DOM environment. You can use it from Eclipse or from a Chrome or Chrome-compatible debugger on the remote desktop. It can be used with apps that create their own webView.
However, you have to install a few files -- but probably no more complicated to use than weinre. it does extensively modify the JS files (on the fly, transparently to the user) to enable all this debugging -- webKit really should support javascript debugging natively.
Your question shows an issue with altering CSS, which weinre does well. I didn't see that weinre supported debugging javascript (ie breakpoints and singlestepping)