Most Minori games? They always have twisted incest routes in Minori games that are as much about people's reactions as they are the relationship itself. Just look on vndb for any Minori game with the incest tag or a sister heroine.
To a more comical extent, any Clochette game with a little sister has an incest route, usually with the little sister being an obsessive brocon who doesn't understand propriety... there usually aren't any huge obstacles to the relationship though, since most people around them are usually aware of the sister's feelings and are at least reluctantly supportive.
Soshite Hatsukoi ga Imouto ni Naru has a lot of messed up characters and two 'imouto' paths, both of which have their own issues that are pretty serious. Honestly, this is one of my major recommendations for imouto routes in general.
World Election has a decent imouto route, but it is similar to Clochette games in that there aren't any huge obstacles.
Yorite Konoha wa Kurenai ni has an imouto route that isn't my favorite, but it does deal with those issues to an extent.
Unmei Yohou o Shirase Shimasu has a seriously, badly twisted imouto route that deals with the issues you mentioned, along with a lot of psychological trauma and the protagonist having been a total a-hole as a kid.
Reminiscence has the single best sister route ever, and while there aren't any social issues involved, there are a ton of hidden issues between those two that are pretty messed up and horrifying.
Kanojo-tachi no Ryuugi is another one with pretty heavy-handed imouto routes, though the reasons are pretty evident early on.
Real Imouto ga Iru Ooizumi-kun no Baai
Koiiro Soramoyou
Tayutama (the original, not the localized one)
Yome Sagashi ga Hakadorisugite Yabai! is another good choice, though this one again is less about social issues than adjustment issues. (really, any of the Yabai! series will work, since the imoutos are all brocon heroines that have a lot of internal hangups)