I think Java (version 1.3.x and up) is a robust programming language and environment. However, Java applets running inside IE are less robust. Javascript is a programming language supported by your browser; It has nothing to do with Java.
You should really be running TWS as a standalone application; That would eliminate any issues with your browser. Re: problems with reconnect, it is much more likely that problems are related to logic bugs in IB's TWS source code.
I hope people aren't using Java as a scapegoat. The benefit of Java is that TWS can run under both windows, linux, etc. without a recompilation. If they would offer a standalone API (that doesn't require TWS running), then it would be simple to write applications on different OS like Linux.
Fleance