Hm, it was our intention to sell the game for the same price in both places; in fact, if you are on Steam, you are not allowed to sell your game anywhere else for less than the Steam price. Nobody is allowed to undercut Steam! Are you sure that buying the game via stonehearth.net yields a lower total price? If so, it may be the result of taxes, currency, or other things outside our control.
We do not intend to ruffle any feathers, we just offer the game in 2 locations: Steam and Humble Bundle (via both Humble’s page and our widget). In both locations, we package the game as is standard on either location (for the same price). (Update: Some people seem to think that the Steam version has DRM, because you need to be signed into Steam to play Steam games, but our goal was to never put any kind of DRM on SH to start with, so retiring the direct download version seems a little weird to us.) There are many people who could not buy the game via Humble Bundle (for payment option reasons) who told us they would only buy it on Steam, so hopefully the two versions offer more options for more people.
Thanks for letting us know about the perceived difference though! We’ll try to let people know that our intent was for the two versions to be equal in price.