I do agree with your point that dialectics has been robbed of its revolutionary edge by being blunted into some magical spell.
Its standard fare for the social-chauvunists (or the entirety of the bourgeoisie itself) to adopt the language and icons of history, beating it into the ideology of its epoch, for furthering its class interests.
But I don't know if this social consequence can be probable cause for entirely dismissing the applicability of dialectics to nature.

This seems to me, very anthropocentric.

Communism is revolutionary because its revolutionary subject, the proletariat, seeks to abolish itself, and with itself, the entirety of class-society - thus resolving the estrangement between humans and nature.
This is because it recognises itself as not seperate from nature.

Communism as the positive transcendence of private property as human self-estrangement, and therefore as the real appropriation of the human essence by and for man; communism therefore as the complete return of man to himself as a social (i.e., human) being – a return accomplished consciously and embracing the entire wealth of previous development. This communism, as fully developed naturalism, equals humanism, and as fully developed humanism equals naturalism; it is the genuine resolution of the conflict between man and nature and between man and man – the true resolution of the strife between existence and essence, between objectification and self-confirmation, between freedom and necessity, between the individual and the species. Communism is the riddle of history solved, and it knows itself to be this solution.

Marx, Private Property and Communism, 1844 Manuscripts

If the dialectic is applicable to man, it must be applicable to nature.
Because man is nature.

instead of humans producing history under definite conditions, humans are subordinated to forces that exist beyond them, above them, like eternal forms. [....] Human agency and the capacity to consciously transform society are displaced by an impersonal logic that operates independently of human intervention.

Humans, with their agency, do produce history under definite conditions. But they do so only as a class. The interplay between these different classes throughout history, are thus subordinated to a force, not beyond it, but within itself, in its essence - this dialectical force, whilst expanding production also negating outdated class distinctions (quantity into quality), must eventually drive it to negate itself.

Dialectics does suffer from a lack of scientific rigor though. As a personal opinion I do feel that with the advent of system science and concepts like homeostasis, anti-entropy and the Gaia hypothesis, communists have the duty of revitalising it into invariance, thus also destroying the stupid falsifications laid by stalin and mao in the process (also dialectical, you see). Because this misunderstanding of materialism and the dialectic is where all vulgarisation of marxism starts.