It is important to understand that when they said "javascript" they almost certainly meant "DOM". All mainstream javascript engines, including Carakan (the current Opera javascript engine), are very compatible with the standard and with each other.
On the other hand, DOM APIs are rather less interoperable across browsers for both historic (lack of clear standards until recently) and technical (larger surface area, faster pace of addition, lack of proper testsuites) reasons. Therefore they are by far the more likely place to run into an interoperability issue.
I have written a heavy JS proprietary Ajax app, and opera was very easy to get working.
Opera really follows the standards, and if I found any bugs they were often an indication of a fragile part of the code that needed fixing (Opera was very useful for finding dodgy areas of my code).
Of course it depends upon the features one is trying to use, not just the quality of the code :-)
At http://my.opera.com/ODIN/blog/300-million-users-and-move-to-... they state they're switching because they feel it is a waste of resources to maintain their own rendering engine. I'd be surprised if the JavaScript engine was a big factor in their decision. The vast majority of "JavaScript" problems encountered by web developers are either problems with the DOM implementation in general. A smaller portion are in the binding between the DOM implementation and the JavaScript language, and fewer still are in the JavaScript engine itself.
A year ago I worked on an app with heavy JS frontend and frontend guys told that they can't make it work properly on Opera.