Unfortunately, I have not been able to find even a decent resource on the general topic of creating extern definition files. So, please take this with a grain of salt, and let's hope someone more knowledgeable can come along and clear things up.
My belief is that using an unmodified JS file as an externs file will most likely result in an overeager list of unmanglable names being used when minifying your compiled JS. There's plenty of names mentioned in the jQuery sources that are not meant to be called publicly, and I expect that the closure compiler doesn't know that.
Another problem arises due the extremely dynamic nature of JS -- it's not possible statically to tell what fields an object might have, since they can be added dynamically, etc. It would be trivial to write a contrived example where the compiler couldn't know not to mangle a particular name.
Aaaanyway, the best solution for your specific case is to just change your :externs to ["externs/jquery.js"]. The jayq JAR contains this resource, and it has already been hand-built to be used as an externs file.