How it works today is what matters to users. Tomorrow the native stack will just make use of more hardware features, it will still be faster, and we'll still be having the same conversation that we'be been having with JS ideologues for 10 years now. "Someday ..."
This is what the XML ideologues used to say too. The problem wasn't XML, it was the libraries, or the lack of dedicated XML processing hardware. Then someone realized that if you got rid of the core complexity -- XML -- you could stop layering on piles of additional complexity while trying to work around the root of the problem.
Someday...
Sandboxing is certainly a good thing, but it's not perfect. Sandboxed code still increases the attack surface. The rationale behind pdf.js is that, because it's almost entirely unprivileged JavaScript, it's unlikely that there's a way to exploit a browser in the presence of pdf.js that wouldn't work in the absence of pdf.js.
Java has had multiple drive-by exploits discovered in just the past few months, which by definition don't require confirmation.
I was inaccurate, however. Java is almost certainly the cause of most exploits, but I daresay that user inexperience (to put it kindly) is probably the source of most infections. Touchè.