I'm not sure why you think Pillage doesn't work against ultra-thin decks. The classic ultra-thin deck - Bishop/Gold/Silver/Silver/Province is utterly hosed if you keep discarding the Bishop. Now if the Bishop deck sets up faster than your Pillage deck, by all means it won't work, but you can really tank a Bish/Chap deck by discarding the Chap early, the Silvers mid (so they can't buy Gold), and the Bish late.
In general ultra-lean decks lose a lot of steam with consistent Pillaging of the trasher. Say you are running to Kc/Monument and you both open 5/2. Pillaging his Chapel on T3 or T4 gives you a turn and a half (the reshuffle is bigger) to do whatever you want (e.g. get there first). Which is another nice thing about Pillage, if you are going for an expensive ultra-lean deck, Pillage buys you a turn AND increases you total money by six. So say you have two silvers and a Steward going for Kc/Forge/Fortress, you buy the Pillage at 6. Play the Pillage, buy a Fortress (make your opponent's turn suck). Now you have Silver/Silver/Fortress/Spoils/Spoils/Steward - Get a Forge (return a Spoils). Forge a Fortress and a Silver (gain a Kc, gain back Fort), buy a Fortress (return a spoils). When you just buy gold, unless you need gold, it is another card cluttering your ultra-lean deck. Pillage is a quick infusion of more cash, and it removes itself after you don't need it.
In recap, ultra lean decks normally can be attacked at the trasher, at the 5 or higher price point (discard his silvers so he has to wait a turn for a Kc), and against powers cards late game (particularly if it is a no-draw ultra-lean combo but also if he its non-terminal draw with relatively sparse villages or the converse).