Dealing with good CND rogues
If its WvW, and there are critters around, then you don’t have a lot of options. If it is anywhere else, sans other people and critters and mobs, then it always comes down to how well you anticipate and avoid the C&D. I know that is useless advice really, as learning to avoid the C&D and getting their timing down is much easier if you actually play a thief and understand it.
Also really really good thieves are nearly unstoppable, because if they time their skills for after your dodge is down, you are without vigor and likely unable to avoid the C&D.
Retaliation doesn’t do much at all. Your best bet is to fear hide in the shadows, and hope you have enough burst to take him down in 3 seconds (assuming his house, and blinding powder, and shadowstep are all down).
One small tip that I usually tend to do is save staff#5 for when the thief pops Shadow Refuge. It’s not much but it will almost always fear the thief out of SR which makes him waste a 60s CD skill and prevent him from getting the stealth and heal from it. As you mentioned, staff is a good choice since besides this you can also use marks to spot the thief in stealth to give you a bit of warning.