I disagree. The usage has detached from the historical context of the original (mis)quote, and there’s no good reason for it to be eternally enslaved by it. This is also reflected in entries like [0] and [1]. Indeed, the Wiktionary entry notes that it
may “be used ironically, in negative view” of the Hundred Flower Campaign, which in turn means that by default that context isn’t implied, and instead as a proverb it merely has the meaning described above in the entry.
[0] https://en.wiktionary.org/wiki/let_a_thousand_flowers_bloom#...
[1] https://playjustsaying.com/idiom/let-a-thousand-flowers-bloo...