Could you please try it again with a newer version of dolphin? I think this issue is fixed in revision 3.5-2421.
Even as far back as 3.5-367, I'm not seeing any flickering. I was on the Open CL backend, with resolution at max, and progressive scan enabled (it really smooths out some textures). And that's with EFB to texture.
I did see a few flickers in v3.5-2318, and in versions around it.
Try the newest build anyways, enable progressive scan, and then test if EFB to texture gets rid of the flicker.
Never mind, newest revision fixes it :-)
I like teh new DSP :-)