Good discussion at https://politics.stackexchange.com/questions/82572/why-are-s... about the issue.
A quick Googling doesn't find me a counter-estimate from Israel. Given the very clear evidence of large scale bombardment of the Gaza Strip (Israel claims 6,000 bombs dropped, and Hamas is known for favoring populated areas; https://www.wsj.com/livecoverage/israel-hamas-war-gaza-strip...), counts in the thousands seem very plausible.
I don't doubt they include Hamas fighters, but I do doubt that Israel's targeting has been so effective and precise the deaths are mostly Hamas. US intelligence estimates 20-25k Hamas members (https://www.dni.gov/nctc/ftos/hamas_fto.html); I don't think half of them are likely to have been already taken out.
Also, as a percentage of civilian population Gaza deaths are very close to Iraq deaths, except way less dead children in Gaza vs Iraq.