might be best to keep away from overly stressing the whole Europe angle, from the perspective of a political system, for the many reasons that have previously been discussed on this list (people feel too strongly about it).
So maybe the best thing to do [read: least controversial] is simply to pick another obsecure animal and trust that just about everybody is going to get to know what the FSFE logo is pretty soon anyway. After all, they accepted the GNU logo and the symbolism of that is not in the least obvious. Or indeed one might go for a different sort of gnu. Or preferably some creature with optional bright colours such that you can happily stick it on a T-shirt. A puffin, for example... something geeks would want to wear. Nice, bright, simple, easy to draw... ;-)
If you think FSFE isn't going to get sufficient media attention for people to recognise a symbol so divorced from intuition, I question the probability of their spending time to interpret any complex symbolism either... if this is true, the only real possibility is to use a logo with 'FSF Europe' quite clearly written on it so recognition from memory is unnecessary.
Em