Like Hammy said, for secondary, unless you store your chocolate in your dirty clothes hamper, it'll be fine to just toss it in.
But do whatever makes you comfortable. It's certainly not wrong to say nuke it in the microwave just till it melts, then throw that in.
Thanks for the help. I've heard about people just throwing adjuncts in ad other sterilizing them. The one plus I see to sterilizing with whiskey is maybe it will impart a slight whiskey flavor. Mmmmm... Chocolate stout with a slight whiskey flavor... *drool*