Silence says you are immune to sonic and language-based attacks.
And Holy word is a [good, sonic] spell.
Thus I would say it protects you. Simple as that.
I've wondered about this with sonic spells for a while now. If a creature uses the Holy Word spell, for example, and I am in the area of a silence spell, does it affect me? What if I am deaf and cannot hear the sonic components? I'm specifically referring to spells that have the [sonic] descriptor.
As above, Silence (the spell) blocks spells with the Sonic descriptor.
As for deafness:
Sonic: Sonic effects transmit energy to the target through frequent oscillations of pressure through the air, water, or ground. Sounds that are too high or too low for the humanoid ear to detect can still transmit enough energy to cause harm, which means that these effects can even affect deafened creatures.