Sorry, this isn't a semantic conflict on the meaning of "prevent" is it?
A library adopting the AGPL license has the effect of making it impossible for closed-source non-commercial projects to use it, even without modification.
> If you do not like the obligation it places on you in exchange for using the work of other people then don't use it.
Commercial projects can afford to pay, open source projects don't need to.
Charities, research institutions, etc can't afford to pay, and usually can't open source their projects.
If we move to an industry where AGPL is standard without any exemption for closed-source non-commercial use, we prevent the usage that nobody would object to.
No one is entitled to use other people's work free of obligations, although they are sometimes allowed to do so through the generosity (and sometimes naivety) of others.
If you do not like the obligation it places on you in exchange for using the work of other people then don't use it.