As you said above, the word "bob" means fencing and you want to know how this can have a double meaning related to homophobes.
This is what I see the 2 meanings as:
1. fencing, as in taking out your fencing sword
2. take out your penis, as penis would be another word for sword in plays/books such as the one you're reading - this would be relating to gays if the convo was btwn 2 men
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The anger comes from the misplaced objectives of both North and South. No party, according to this speech, was willing enough to see peace as a worthwhile alternative to a war that was inevitable given what each thought. This thought comes at the end of paragraph 2.
The history of the Bible's response to this kind of thing is put there to shift a proper religious interpretation of what the war actually meant, and what prayer actually accomplished, and how a loving God would respond to such prayer.
The shift is absolutely concluded right at the beginning of the next paragraph, It, in fact, begs the nation to seek healing. Lincoln hopes that the war will be put away quickly and the union will once again be one.
Word Choice. Hope this helps!