While I am not an atheist, these do not seem like very deep questions to me.

1) we have only the word of whoever wrote the Gospels that the disciples saw a resurrected Jesus, and three of the Gospels are synoptic - i.e., they clearly derive from a single common source. As such, there are really only three sources who claim Christ was resurrected in the Bible. (A) whoever is the original source for the synoptic gospels, and we don't know who that was. (B) the Gospel of John, probably written by John the apostle (though it never says so). (C) Paul's letters. And Paul didn't see the resurrected Jesus except in vision. Therefore, your numerous "disciples who saw Jesus" drop down to two people (the unnamed synoptic source and John), and I can claim that they were either mistaken or trying to deceive.

2) I agree that the existence of Nature proves a Divine Source. Like I said before, I'm not an atheist, and so this is obvious. But it doesn't demonstrate that this Divine Source is any friend to man.