It depends on which entities you have configured the color coding in your JScript. If it's on the entities that use the new Process-Driven UI, then no, JScript is not supported.
Also, you can not guarantee that the JScript you have written will work in other browsers, as changing styles (such as a controls color) in the CRM form is not supported.
Moreover, if the methods you use to change the colors is written using CRM 4.0 methods, this will also break after UR #12, though some of it may work if you enable HTML Component Support.