You're killing far, far more civilians than your enemy does (unless of course you now declared said civilians the enemy as well). You can't say that about any allied nation in WW2.

Also, what do you do if the enemy decides to deliberately surround himself with civilians so as to maximize the civilian casualties from attacking him?

The same as what you already do when they surround themselves with Israeli citizens.

The Imperial Japanese Army posed a significant threat to US interests and long term security, expecially given that it was allied to the other Axis powers. Still, many people believe that the nuking of Hiroshima and Nagasaki was excessive and immoral.

Anyway, WWII is a poor analogy for the Israel-Gaza conflict: the threat level Hamas exerts on Israeli security, or even economic welfare, is minimal, therefore the damages to the security ang welfare of Gazans caused by Israel "self-defence" operations are seen as greatly disproportionate.

In fact, it is often argued that Israel military actions are even inefficient at accomplishing their stated goal of protecting the security of its citizens, as opposed to other non-military options that Israel has, such as avoiding to provoke Hamas to fire rockets by imprisoning and killing its members in the West Bank without good cause, or finding reasonable terms for a truce (face-saving for both parties) once the mess had been started.
In the medium-long term, it can be argued that it would be in the interests of the security of Israeli citizen that their government negotiated a permanent political solution with both Fatah and Hamas.

Another important way in which analogies based on traditional warfare fail, is that Gaza or the West Bank aren't countries separate from Israel, they are regions under Israel military occupation.
Gaza has some level of autonomy, with Hamas acting as a de facto government for day-to-day administration and law enforcement, but Israel keeps control over Gaza airspace and access to international waters, which still counts as military occupation under international law. International law, which many people find morally reasonable, also says that an occuping powers has special duties to protect the civilians of the regions under occupations: since they don't have a fully sovereign government taking care of their interests, the occupying power must take the burden on itself.

In any case, international law, and I would say common morality as well, condemns the killing of civilians if it doesn't accomplish a reasonable and "proportionate" military objective.
The Allied firebombing of Dresden, and maybe even the nuking of Hiroshima and Nagasaki, can be argued to have accomplished valuable and proportionate military objectives despite the high number of civilian deaths, as they greatly damaged the enemy industrial capability and hence their war effort.
In the current round of Israel-Gaza conflict, thousands of Gazan civilians have been killed, including children playing football on a beach, people in the premises of an UN school, etc. Israel officially claims that some of these deaths were accidents and blames the others on Hamas usage of human shields. Maybe that's techically true, but when you are bombing and shelling an heavily populated area, a certain amount of "accidents" and more or less deliberate human shielding are inevitable. You know that a lots of civilians are going to die, and you need a damm good military objective in order to justify it.
What military objective is Israel accomplishing? Hamas is still firing its rockets, which are still extremely ineffective at killing Israeli citizens. Eventually, Israel may stop the Hamas rocket launches by destroying all the caches and smuggling tunnels. And it will take only a couple of years for Hamas to replenish its arsenal, and for each dead militant, Hamas will be able to recruit three from the enraged population.

This combination of large loss of civilian lives and minimal accomplishment of military objectives, particularly given the status of Gaza as an occupied territory, are the reason why people argue that Israel actions are disproportionate and doubt Israel good faith in its claims that it is trying to minimize civilian losses.

The alternate, uncharitable hypothesis to explain Israel behavior is that it is trying to maximize Gazan civilian deaths while maintaining the plausible deniability it needs in order to keep US financial and military aid and support in the UN Security Council. Thus Israel can't nuke the Gazans or put them into death camps, but, according to this model, it would love to.

This model, where all the Israeli are bloodthirsty monsters, is overly uncharitable. Real world politics is complicated:
Israel has an almost pure proportional political representation system, which results in coallition governments where small parties that can switch sides are greatly favoured. The current ruling coallitions has nationalistic and religious parties which are apparently made of kill-all-Arabs bloodthirsty monsters, and the government as a whole has to balance padering to a broad electorate, which includes bloodthirsty monsters that vote for said parties.
Overall, the average Israeli voter is probably not a monster, but finds it easier to cooperate with the Israeli monsters rather than with the Palestinians, who also have their share of kill-all-Jews monsters.

Anyway, this comment is quite long and discussion of contemporary object-level real-world politics is discouraged here, probably with good reason. The Israeli-Gaza conflict is one of the most divisive political topic ever, therefore I'm not going to carry on this discussion any more.

Hamas's rockets don't kill many people, but...

Don't use political examples in a non-political argument. There are always plenty of others to choose from.

It's not as if they're blowing a puff of cigarette smoke towards you and increasing the probability by 0.001 that you may someday get cancer--people actually die from those rockets.

How many Israeli civilians have been killed by rockets since Operation Protective Edge? Three. Out of a population of 8.1 million.
If Hamas hired tourists to go to Israel and puff smoke in crowed areas it would probably have a greater effect on the Israeli mortality rate.

Furthermore, you left out the part where the guy deliberately shot at you from a crowded neighborhood so that the only way to defend yourself is to endanger the people around him.

As opposed to seeking a political solution?