Nukes are a pretty useless solution against anything sufficiently advanced, because they would presumably be able to protect against them (eg. God makes a plane of existence where fusion doesn't work).
Honestly surrender against a being that powerful (without technology thousands of times more advanced), surrender is the only viable option. Hell, it might be the only option at all given that it could forceably change everyone's minds to make them surrender.
Okay, I'd like to present you with a challenge. Think about what being God is like. Imagine that there is nothing except you and infinite power. Now, create something perfect. Do you think that's possible? Have you done better? I'm not claiming that God is perfect, far from it. I simply think we are in no position to judge a divine being with infinitely more knowledge and experience than each of us, and if he has made mistakes, then quite honestly, why can't we forgive Him?
Its easy, I would use my omniscience to know exactly what to create, and my omnipotence to create it. Now, its clearly very different if he lacks omniscience. But he doesn't, thus the quandary.
I personally find the argument that "we live in the best of all possible worlds" (to quote the old philosophical argument about the goodness of god) to be a bit ridiculous, but its not really possible to disprove.
After all it is correct that any bad things could theoretically be necessary for better things later on or that happened in the past.
I don't like it because it doesn't line up what humanity has perceived of reality at all (eg. randomness and the viciousness of the universe and evolution), but it is philosophically consistent.