The Pioneer anomaly is being studied of course and there is as of yet no explanation. According to this paper
http://arxiv.org/abs/gr-qc/0205059 the most likely cause is the spacecraft design itself.
It would be difficult to use the Pioneer spacecraft for studies now since it is difficult to pinpoint their eact position to the level you would need to test your photon theory.
I hope there is some other way to test your theory - it's not often that spacecraft is sent on planet hopping missions like these, and
AFAIK not a single one is being planned at the moment (at least none has left the drawing board)... ESA is currently focusing on Venus and Mercury (and Mars, of course), and NASA might eventually launch their Pluto mission but who knows when.