To be fair the EFF is a non-profit organization (made up of lawyers, no less) that has to follow strict legal and tax standards. Can you even imagine the tax paperwork for bitcoin? Even if they bought office supplies or something with the bitcoins instead of selling them on Mtgox, it still wouldn't be pretty.
That's what I was thinking as well. Charitable donation tax code varies from state to state. They might, in one state, have to record donation sources over a certain amount (maybe not by name, but at least demonstrate if it was personal, corporate, or political).
But how do you tell where a donation is coming from with Bitcoin? They would first have to set up a storefront, and give each donor a unique address and have them provide at least some info for the books.
That, and there are some recent shady donation laws that were made in the name of anti-terrorism, but could possibly affect them. Google the phrase "geographic targeting orders" for example. Taking one donation that was later proven to be from a terrorist support organization could put their whole operation in jeopardy. It's a fight that would be worthwhile, but the EFF would probably rather pick their battles.