i think this will be more of an allegory of how we are handling the "war on terrorism", with a lot more grey.
I hope not. The premise doesn't lend itself to modern real-life allegory at least not in such a direct manner. One of
BSG's biggest failings was trying to impose real-world allegories on a premise that didn't lend itself to such efforts (and then the producers trying to tell the audience that
they are at fault for making the obvious and natural conclusions about a plotline dealing with, for example, suicide bombers.)
The
V story seems to be more about the dangers of allowing blind faith to control your society - the Visitors are built up into a quasi-religion (which isn't unrealistic for the first alien contact w/Earth if the aliens look and act as nice as the Visitors do). There are some obvious real-life parallels there, but a lot that isn't parallel, and the producers should be careful about how the audience is likely to perceive such things - if you don't mean for there to be a direct parallel, don't use a heavy-handed approach that leads the audience to that conclusion.