Pretty sure the math being done is: 45,000 (Hamas's figure for Gazans killed, which includes both Hamas militants and civilians) / 2,150,000 (population of Gaza) = ~ 2% of the population killed.
Plus there have also been 50,000+ births in Gaza since the war started so it's actually possible there are more Gazans alive today than on October 7th (although slightly fewer in Gaza itself, as 100-200k were able to leave).
Seems a little difficult to argue extermination is the goal if that's the best they can do after 14 months of brutal war.
The Gaza Health Ministry's reporting of casualties have been found to be generally accurate (
https://www.aljazeera.com/news/2023/10/27/un-says-gaza-health-ministry-death-tolls-in-previous-wars,
https://www.aljazeera.com/news/liveblog/2023/10/24/israel-hamas-war-live-fuel-shortfall-could-force-un-to-halt-work-in-gaza-2,
https://www.washingtonpost.com/world/2023/10/24/gaza-death-toll-palestinian-health-ministry/) but do have some problems with them when considering the dead from this conflict.
These numbers only count direct deaths of Palestinians (those who were shot, died of shrapnel, bomb/explosion, etc.) verified by doctors. They do not count the tens of thousands of people who have gone missing since the beginning of the war (20,000+ children alone reported missing by June this year -
https://time.com/6992508/gaza-children-save-missing-famine/). They do not count deaths by starvation (estimated at more than 60,000 back in October -
https://www.doctorswithoutborders.org/latest/how-year-war-has-devastated-gazas-civilian-infrastructure. They do not count deaths by thirst. They do not count deaths by preventable disease (caused by destruction of sanitation facilities, lack of clean water, destruction of hospitals and medical centers, prevention of medical aid from coming into the country). It doesn't include those who have died of exposure (remember that more than 2/3rds of all buildings in Gaza have been destroyed or damaged in this conflict -
https://unitar.org/about/news-stories/press/66percent-total-structures-gaza-strip-have-sustained-damage-unosats-analysis-reveals). Because fewer than half of Gaza's hospitals remain functional (
https://www.doctorswithoutborders.org/latest/how-year-war-has-devastated-gazas-civilian-infrastructure) and those that remain functional are running well below capacity, this count (which depends upon doctors to verify the death and cause of death) is likely becoming a more and more significant undercount as fewer and fewer people are able to make it to medical centers. You also mention the 50,000 children born in Gaza since the start of the war. How well do you think those infants are doing given that the whole population of the Gaza strip is currently starving, does not have access to enough water each day to survive, and has virtually no medical care? Remember that none of these deaths would be considered casualties of war from the health ministry and be in the 45,000 figure you're referencing.
It seems that dividing the number reported by the Gaza Health Ministry by the population of Gaza is certain to produce a radical undercount of the number of dead.
As to the Israeli extermination of Palestinian civilians in Gaza . . . it wasn't exactly a secret plan. Israel's government has been vocal about the desire to do this:
"We are imposing a complete siege on the city of Gaza. There will be no electricity, no food, no water, no fuel, everything is closed. We are fighting human animals." - Israeli Defence Minister Yoav Gallant
"Gaza won’t return to what it was before. We will eliminate everything." - Israeli Defence Minister Yoav Gallant
"There are no innocent civilians in Gaza," - Israeli President Isaac Herzog
"One of the options is to drop an atomic bomb on Gaza." - Amichai Eliyahu, Israeli Minister of Heritage
"Those are animals, they have no right to exist. I am not debating they way it will happen, but they need to be exterminated," - Yoav Kisch, Israeli Minister of Education
"Bring down buildings!! Bomb without distinction!! Stop with this impotence. You have ability. There is worldwide legitimacy! Flatten Gaza. Without mercy! This time, there is no room for mercy!" - Revital Gottlieb member of the Israeli Knesset and member of Benjamin Netanyahu's party
"As long as Hamas does not release the hostages it is holding - the only thing that needs to
enter Gaza is hundreds of tons of explosives by the Air Force, and not an ounce of
humanitarian aid." - Itamar Ben-Gvir , Israeli Minister of National Security
"No one in the world will allow us to starve 2 million people, even though it might be justified and moral" - Israeli Finance Minister, Bezalel Smotrich