In the last scene in New Hampshire, Tom says to Kay: "If you told Michael what I’ve told you today, I’m a dead man.”

Would Michael really have him killed? And if so, why would Tom risk his life just to safe Michael's marriage?

That is a very good question and I really like the romanticism of this conversation and especially this sentence. I think if Kay would have gone straight to Michael and told him what she had heard maybe Tom would have been in real trouble (let's say killed, I do not think it matters) but I think Tom basically took no risk, he knew that Kay would not tell Michael this directly. On the other hand Michael probably had an idea what happened between Tom and Kay (he was smart and very receptive for changes in people's behavior)but was ok with it until nobody talks about it.

For one thing I was always wondering why Tom hesitates to tell this "final truth" though, he has to tell Kay somehow that this conversation never happened.

I think Tom not being Sicilian, He would of being killed anyway for knowning so much of Information being an Outsider.

I think Tom said that because he wanted to emphasize to Kay that "you and the children are the only people on this earth he couldn't harm."

Michael obviously sent Tom to New Hampshire to convince Kay to come back. I don't think he specifically told Tom to convince Kay by revealing that Michael had Carlo and Tessio killed--and why he had them killed. So, if what Michael told Kay caused her to hate Michael, divorce him and take the kids, Michael would have blamed Tom. And, yes, he might have had him killed, rationalizing that Tom "couldn't be trusted" with such dangerous secrets.

Kay already knew. Tom explained the reasons for it using a hypothetical.

I think the answer is yes. He killed his blood brother, I think if Michael thought Tom did something out of line, then he would have been killed.