Question: without the experience of the Nazis to totally discredit it, does eugenics remain a field of respectable scientific study until the modern day?
Oh hell, yes. Eugenics is alive and well. In many Western countries, it is a tad controversial, seen as a good thing that can definitely be abused and that our forebears didn't really proerly understand, causing some unfortunate side effects. An uneasy alliance of Socialist and Catholic activists oppose it as a policy principle, but most people, while they may admit that forcible sterilisations were a bit much (they don't know about the mandatory abortions of mid-century), generally don't see a problem with ensuring future generations are born healthy. It isn't a high-profile thing any more. It was in the first half of the twentieth century when it was married to all kinds of half-baked racial theories, but as its defenders make clear, that was not 'real' eugenics. 'Real eugenics' is based on a solid understanding of genetics. It is studied both as a field of medicine and of social studies. "Humangenetik und Populationseugenik" is a Facharzt qualification that students come from all over the world to obtain. Berlin, Marburg, Göttingen, Tübingen and Dresden are the leading research centres (Tübingen was where DNA was first isolated). Social workers have a mandatory course in eugenics and can qualify as "FamilienberaterIn" with nurse-level training in child care, general medical practice, and practical eugenics. Many other countries have similar systems.
ITTL, the face of eugenics in Germany is not a sadistic SS officer vivisecting Jewish children, it is a smiling lady (social work is overwhelmingly a female occupation) explaining to hopeful couples what financial aids are available for starting a family, where to apply for maternity leave, what medical tests should be taken prior to and during pregnancy, and what medical interventions are indicated should ("We do all in our power to prevent it in advance, but there are so many things we do not know yet.") the fetus show abnormalities or worse, if the defect went undetected until birth. It looks nice, many people think it is. Many practitioners generally try to be helpful. Most eugenicists get into the field because they love children and want to see them healthy and happy. They have spent years perfecting the ability to talk hesitant mothers-to-be into abortions or relatives into euthanasia. They are 'good people'.
By the early 21st century, genetic screening is a routine procedure early in the pregnancy, abortion in the event of abnormalities is covered by health insurance, and this has reduced the number of child euthanasia to a very low figure (all euthanasia requests must be made through a medical doctor and screened by a commission). That is what progress looks like, I guess.
About the Lithuanians, I thought they were considered as loyal as Germans, since they had been in Prussia from the start. Like how the referendums in East Prussia had the Protestant parts want to stay in, or something.
AFAIK the Lithuanian minority was never actively combated or 'denationalised' the way the Poles and French were. It makes sense - the Germans have long had a collective soft spot for the people of 'the North' and tended to romanticise them. That said, they would only be considered German if they actually assimilated culturally and linguistically. No doubt many will - many members of minorities did IOTL and the German government honoured the deal (then). You will see loads of Lithuanian families adopt German names, speak German at home and send their children to German schools. But Lithuanian identity will no doubt remain, and grow in the course of the twentieth century as people become a tad less nationalistic.
new question how are the wittlesbach and Bavaria doing?
Those are two different questions.
Bavaria is doing fine. It is not comparable to the stellar economic success story that the Cold war made it IOTL, but it is a thriving part of Germany with excellent universities, large industrial towns with both traditional and future-proof manucaturing, a major urban centre in Munich, significant tourism appeal, and the reputation of being the 'nicer' part of Germany. More 'gemütlich', more soulful, less of the hard edges of Prussianism. Berchtesgaden draws droves of German families from the Ruhr and Berlin longing to escape the moloch, skiing and mountain hiking are popular upper-middle-class sports, and the Oktoberfest is one of Germany's biggest tourist attractions, bigger than Karneval in Cologne or Sedanstag in Berlin. The Bavarians know how to party.
Of course it's not all sweetness and light. Many rural areas are still underserved and poor. Traditional cliques of landowners, industrialists, priests and officials (often from the same families) monopolise political decisionmaking. Education is patchy: excellent universities and top-tier Gymnasien coexist with rickety village schools for the rural poor. The influence of the Catholic church on social life outside the cities was long-lasting and often pernicious. Yet for all the justified criticism of the 'black stranglehold', it also saved Bavaria from some of the more egregious abuses of the twentieth century eugenic movement.
The Wittelsbach now - that is a different story. The royal family made the unfortunate decision to try and base their continuing political influence on traditional rural elites and the church. That backfired as Bavaria increasingly industrialised and urbanised, and the kings did not deal well with the situation. They failed to align themselves with democratically legitimated factions the way the Hohenzollern and other ruling houses did. Politics in Bavaria were characterised by decades of confrontation between town and country, liberal pro-democratic and Catholic royalist, and the Wittelsbach family's image suffered badly as a result. They were one of the dynasties that did not abdicate responsibility gracefully. The king still reigns in Bavaria, but he does not rule and has few enough friends. Even the church is increasingly divided between conservative hardliners and squishier moderates, the villages that were the favourite recruiting ground for police and army are shrinking or turning into suburbs, and even many very conservative Bavarians see the (distant, mighty) emperor rather than the (embarrassingly close and often impotent) king as the focus of their loyalty these days.