You have to keep in mind that the EFF get into some very important political battles and earn some very fearsome enemies.
In DC politics your enemies will not kill you but they will sue you, or they can do even worse -- they can ask their friends in Congress to open an investigation or to ask the DOJ to do so.
Thus, the lawyers for the EFF have to be really really careful and make sure that there are no open avenues of attack. When you are potential target, you have to be much more cautious than you would usually be. Especially if your enemies are very powerful and well connected lawyers, powerbrokers and publicity people. These people can take the slightest infraction, real or imagined, and weave it in a complex and snowballing story that ends with you having lost all credibility.
Note what happened to Julian Assange.
So no you cannot blame the EFF for refusing to be adventurous vis-a-vis bitcoin.
Furthermore, their change of policy is probably not related to startup money but to the government providing guidance for virtual currency.