Yeah, you definitely have flexibility. Stage 0: Entrance and Stage 0.543 (http://www.youtube.com/watch?v=y7thxap6Q2o) pretty much directly contradict each other. If you want to go with Suzaku killing Genbu during the invasion, then I'd recommend ignoring the light novels and going with the picture dramas/sound episodes. The PDs & SEs for the first season are all consistent with the series proper (and each other), from what I can tell.

Anyway, in both versions, Suzaku killed Genbu before parting ways with Lelouch & Nunnally. The difference is how far before.