The numbering is a good idea, it makes it easier to tackle..
1. Here's what I don't understand: You like your friend, you obviously think he's a good-guy, but because 'Old Testament God' - someone, bear in mind, who killed people for bringing him the wrong tribute and commanded that the seats that women sit upon while menstruating should be burned - says so? How do you rationalize that God with the God of Jesus, who extended kindness to pretty much everyone save for Tax Collectors and Fig Trees?
2. Yes, according to Atheist beliefs. I'm an Atheist. That's my opinion. I don't quite understand how expressing my opinion - other than it differing from yours - makes what I say an insult and what you say fine and dandy. I don't hate you. I don't even think you're stupid. I do, however, think you're wrong. You're also wrong about the 'Day' thing, which predates the Christian God. And, probably, the Judaic God at that. Seeing as we've always had 'Days'. Days being 'When the Sun comes up to when the Sun comes down.'
I treat what I believe as fact, yes, but you aren't doing anything different. Am I to be held by some different moral standard? Should I apologies for my beliefs every time I mention them?
And, finally, I said 'Let's not play around with genetics' too. I also said 'Let's Learn More'. Let's grow up. Learn to use it.
3. And that excuses past behavior? In that case, why not let this modern form of Muslim Extremism - a very different idea from the 'Love Others' belief of the past - run its course. Come back in two thousand years and I'm sure they'll be very civilized.
4. I believe that people should do something because it is right and not do something because it is wrong. You, as you've said, act in this way. But I'm sure there are others out there who avoid wrong-doings not because of some deeper understanding of what they should do but for fear of what the punishment will be.
And I support this with Crusades and Race Riots that spring up in heavily religious areas, where people twist religion in order to give vent to passions that they ignore and bottle up.
Personally, I think it would be better to teach people Why it is Wrong, rather than simply Tell Them that it's Wrong.