So does this mean Shor's Algorithm is going to kick in for real and ruin all our securityz?
Nope.
First, as I understand it, the D-Wave stuff isn't a system that can run Shor's.
Second, Shor's only ruins security for a certain class of crypto algorithm. There are already algorithms that exist today that a proof against it (e.g the McEliece cryptosystem http://en.wikipedia.org/wiki/McEliece_cryptosystem).
Third, if you're really worried about the man cracking your s3cr3t stuff with quantum computers go pick the right cryptosystem ;-) Plenty of symmetric encryption systems that only get their key lengths reduced (effectively halved) by Grover's algorithm.
I thought both the D-Wave 1 & 2 both had specialist quantum chips that couldn't run Shor's.
They also implicitly state that it's not Shor's which is (to the best of my knowledge) the most effective integer factorisation algorithm for general purpose QCs currently know.
They also say that they "have a factoring algorithm". They don't say that it's actually implemented on running hardware.
I also notice the complete lack of clarification on the followup question that poked on the explicit "executed it on real hardware" question ;-)