isaac asimov, samuel delaney, phillip k. dick, ray bradbury, aldous huxley, frank herbert, robert heinlein, kurt vonnegut, ursula le quinn, alan moore, jack london, (many others) ... all wrote some stuff that could be considered subversive.
thoreau was not a novelist (though "walden" might be considered one, not sure), but he was as subversive as any well-known writer i can think of.
edited to change to a comment, and add:
one novel i especially liked and found somewhat subversive is "interface" by neal stephenson and stephen bury (though i think recent editions of the book use stephen bury's other name j. frederick george).
also ecotopia and ecotopia emerging (a prequel) by ernest callenbach have some subversive elements.