I read the discussion you linked and then calculated a bit and compared with my country. Turns out as you say, that this number isn't very high if it's all-cause mortality.

I don't think it's disputed though that migrant workers are treated inhumanely there. Not that Qatar would be the only community to treat migrant workers as second class people. It seems to be a case of a newspaper resorting to touting some numbers to make a point instead of reporting good information, which is sad.