How can Varys ever return to Kings Landing? He'll be implicated in the murders and the prison break now. Was that a better call than to just go back to the city?
I think he realised that Tyrion's little "scorched earth" policy had burnt all of his bridges as well, and the best plan was to bail while he still had his head. You can imagine Cersai's reaction when she is told "Your dad has been crossbowed to death while sitting on the can, and the Imp-brother that you hate (and was found guilty of your son's poisoning by means of proxy in a trial by combat), seems to have coincidentally escaped from the dungeon!". I imagine she will be a tad miffed and will assume he may have had some help. Probably not a good time to be a despised, nefarious bald eunich of dubious sexuality with a foreign accent, who has just collaborated with the brother/incestious-lover of the psycho Queen regent.
I'm very thick, I did not piece together that Shae and Tywin were banging. Glad he killed them both