Sure, thorium reactors do not appear to immediately allow nuclear weapons - but the scientific and technological advances that lead to thorium reactors are definitely "dual-use".

I'm not entirely convinced of either the feasibility or the ethics of the "physicists should never have told politicians how to build a nuke" argument that's been made multiple times on LW (and in HPMOR), but the existence of thorium reactors doesn't really constitute a valid argument against it - an industry capable of building thorium reactors is very likely able to think up, and eventually build, nukes.