Lincoln believed that slavery would die out within an intact US in time, and that pretty much the only thing the federal government could do was to keep it from spreading to states where it did not already exist. Unlike today, in those days the idea that the Federal government actually had limited power was still taken seriously.
If the slaveholding states were allowed to secede then no pressure could be placed on them to give up slavery, and they might even capture or purchase other territories and spread slavery further. So if the moral imperative is to end slavery, then it's urgent to keep the Union intact. And no, I don't think a country is just a club where a province or state can up and leave whenever it wants. There are times when it's wise to allow this, as Havel did with Czechoslovakia, but generally a country is like the Mafia or a spy agency from the movies: you can't resign.
Habeas: this was a war, but I'm really ignorant of the issues here.
wait to free the slaves, and then only do it in the states that were not a part of the union: see above; you can only do what is possible to do, regardless of your feelings. Lincoln wanted to avoid this war, which was started by the South and forced upon him. Of course many people died.
