Addressing the points maid in the OP:
A) It was a civillian population.
B) I don't see how a nuclear holocaust can ever be right.
C) They could have bombed Tokyo where all the generals lived but chose Hiroshima.
D) The Irony after the bombing America conceeded to many of Japans terms.
A - As others have mentioned, the firebombing of other cities also largely affected civilian populations
B - Seldom is anything done in war 'right'
C - Since Tokyo had already been heavily bombed (it's an obvious target for the reasons you gave, and for the mere fact that it's the capital) so it was never a target for a nuke. The americans purposely kept 4 japanese cities as virgin targets for a nuke, because they wanted to truely demonstrate the power of the bomb. If they'd bombed a city that was already nearly destroyed, it wouldn't have had the same effect. I agree with others here who've said that the nukes on japan where probably about 50/50 motivated by wanting japan to surrender and displaying our supremecy to the rest of the world.
D - For those that don't know the full story, the irony goes deeper than you let on. The reason for the americans making concessions to the japanese after hiroshima was because they couldn't stomach the devestation of the nuclear bombing. They wanted to make it as easy as they could for the japanese to surrender, so they tried to allow them to keep some of their pride. The irony is that the Japanese likely would've surrendered had they not tried to let them off a little bit. The Japanese saw their concessions as weakness, and therefore refused to surrender. After Nagasaki was bombed, no such concessions where made and they did indeed surrender.
I'm not sure if I'm really for or against the bombing. It's difficult to know how history would've gone without it. Maybe russia would've eventually nuked us had we not displayed our might. Maybe the japanese would've surrendered soon anyway, since the war was all but lost for them already. Maybe there would've been less loss of life without the bomb, maybe more. I don't think there's much point in speculating on all that, and am comfortable just leaving it as this - violence is to be avoided, but things aren't always black and white. All we can do is use the war as one data point, and hopefully mankind will use it to create more desirable outcomes in the future.