I'm aware of that, and if there were a risk of acts of hatred against Spanish folk by me using that name today, I'd agree, however we're talking about a pandemic that spanned 1918 and 1919, with the second wave in 1919. Using "Spanish Flu" is, however, clear and well understood.
On the topic of how geographic disease names have often been used in racist or at least nationalistic ways, check out this hilarious map of the geographic distribution of names for "syphilis": https://digg.com/2017/syphilis-name-map