After carefully weighing the ongoing attrocities and future threat of Saddam Hussein before the US invasion against the costs, lives lost, displacements, and follow on chaos due to the invasion, I'm persuaded by arguments against that war. But 3000 vs 1 million is not that argument.In some in particular.
If we go civilian death toll: The Iraq war alone had 150,000 - 1 million civilian casualties, depending on the estimate. Compare this to about 3000 deaths from Islamic terror in the US. We can even compare it to the total death toll of terror worldwide: 190,000 in the last 10 years. Most of them national: People from a country attacking people from the same country within that country.
The US suffered zero civilian casualties due to the actions of the Nazis before entering WWII, and yet the US declared war on Hitler in 1941 and 50 to 80 million died. I've not seen the argument made in mainstream historical analysis that WWII carnage could have been avoided had the US only minded it's business.
Similarly, it is not as if it is known that Iraq under a continued Saddam Hussein would have prevented all the harm related to the invasion . Under a continued Saddam a great many Bathists might have been okay; other Iraqis not so much.
...Saddam has had approximately 40 of his own relatives murdered. Allegations of prostitution are used to intimidate opponents of the regime and have been used by the regime to justify the barbaric beheading of women. There have been documented chemical attacks by the regime, from 1983 to 1988, resulting in some 30,000 Iraqi and Iranian deaths.
Human Rights Watch estimates that Saddam's 1987-1988 campaign of terror against the Kurds killed at least 50,000 and possibly as many as 100,000 Kurds. The Iraqi regime used chemical agents to include mustard gas and nerve agents in attacks against at least 40 Kurdish villages between 1987-1988. The largest was the attack on Halabja which resulted in approximately 5,000 deaths. o 2,000 Kurdish villages were destroyed during the campaign of terror.
Iraq's 13 million Shi'a Muslims, the majority of Iraq's population of approximately 22 million, face severe restrictions on their religious practice, including a ban on communal Friday prayer, and restriction on funeral processions.
According to Human Rights Watch, "senior Arab diplomats told the London-based Arabic daily newspaper al-Hayat in October  that Iraqi leaders were privately acknowledging that 250,000 people were killed during the uprisings, with most of the casualties in the south." Refugees International reports that
"Oppressive government policies have led to the internal displacement of 900,000 Iraqis, primarily Kurds who have fled to the north to escape Saddam Hussein's Arabization campaigns (which involve forcing Kurds to renounce their Kurdish identity or lose their property) and Marsh Arabs, who fled the government's campaign to dry up the southern marshes for agricultural use. More than 200,000 Iraqis continue to live as refugees in Iran."
In 2002, the U.S. Committee for Refugees estimated that nearly 100,000 Kurds, Assyrians, and Turkomans had previously been expelled, by the regime, from the "central-government-controlled Kirkuk and surrounding districts in the oil-rich region bordering the Kurdish controlled north."
"Over the past five years, 400,000 Iraqi children under the age of five died of malnutrition and disease, preventively, but died because of the nature of the regime under which they are living." ...
Who knows how Iraq's future government will evolve. For the last dozen years however, Iraq has been led by a regularly elected parliament and prime minister, with no aspirations for WMD, government financing of terror groups, desire to annex Iran, Kuwait, etc.