Not necessarily. That has been discussed at length many times here and elsewhere. PNaCl's approach is interesting and technically has much merit, but also has significant downsides (startup speed, complexity, size of implementation, reliance on LLVM for something it was not intended, risks of undefined behavior, PPAPI, etc.). It's technically an impressive technology but also one with fundamental compromises.
Instead, an undeniably superior approach could be to start entirely from scratch, not JS nor LLVM nor anything else, and work to design something truly optimal for the use case we are talking about here (code shipped over the network, to run securely inside a browser, at near-native performance, with fast warm and cold startup). That would look very different from both JS and PNaCl, and could avoid the compromises that both have.