The short and simple answer is that Hitler was a politician and the hypocrisy usually goes with the territory for all people involved into politics save for the most unflinching of ideologues, although the latter usually do not achieve much of a success as a significant part of getting one's agenda across is the ability to interact with people and making concessions, especially in democratic or other highly diversified political settings.

Having said that, I believe that the question is based on a false premise, that Hitler, his inner circle or the Nazi government was persecuting disabled people in general or that they were putting ideology before reason, especially before they were able to achieve real political power. You might be also interested in my previous posts, where I have summarily covered the Nazis' position on homosexuality in this thread and their stance towards the disabled in this one.

Treatment of homosexuals in Nazi Germany was not that different from their plight in some other Western European countries, that have had similar laws on their books since decades or even centuries. In Germany, the basis for the outlawing of the same-sex relationships (nominally, only between men) as well as the sexual acts between people and animals was the article 175 of the German Criminal Code that has been introduced in 1871. Over the years, it became treated less and less seriously, what was at least partially resulting from the fact that between the defeat in the Great War and the social unrest in early 1920s, police had far more serious issues at hand. This was also one of the reasons for the active homosexuals to relocate to Berlin, where their orientation was less likely to get them into trouble. Such a situation started to change only after the Nazis came into power in 1930, although the more serious actions were taken only in the latter half of the decade, with the formation of State Center for Elimination of Homosexuality and Abortion (Reichszentrale zur Bekämpfung der Homosexualität und der Abtreibung) in October of 1936, two years after the execution of Ernst Röhm.

Please note that the main problem for the homosexuals in Nazi Germany was not the law itself, as similar legal provisions were enforced in many other countries at the time, but rather the totalitarian character of the government. In other words, a person accused of homosexual relation in, say, England, could have been punished only after a trial, where adequate evidence would have to be brought against him and where he could employ the help of an attorney. In totalitarian Germany, such person could (and many did) have been simply clandestinely arrested even on false pretenses and sent to prison or concentration camp without the due trial by an independent court of law. On the other hand, the totalitarian government could have easily covered up the homosexuality of people they wanted to keep on their side.

Now, regardless of the legal rules or private opinions of the high-ranking Nazis, Röhm was simply too powerful and useful to be disregarded. He was very well-connected, especially in the military circles and rendered extremely important services to NSDAP without which they would possibly be unable to achieve heir goals. He formed the Sturmabteilung (SA), paramilitary organization that was instrumental in securing the power of the NSDAP later, managed to hide the large number of light and heavy weapons so they were not found by the Allied commissions overseeing demilitarization of Germany after the Treaty of Versailles (the amount was enough to cover almost 30% of Wehrmacht's needs in mid-1930s) and was able to buy the Volkischer Beobachter newspaper that later became the main propaganda tool of NSDAP. Last but not least, he was one of the first fascists elected to Reichstag. In other words, he was extremely useful for the Nazis and rejecting such a figure only on the grounds of his sexual orientation would have been a political suicide. It is worth noting that although many high-ranking members of military, such as Gen. Erich Ludendorff knew about Röhm's homosexuality and were openly critical of it, Hitler claimed that these allegations has never been proved and did not hold it against his political colleague.

It is also not true that Hitler or the NSDAP in general were inclined to eliminate all disabled people and any physical disability was a reason for ostracism or persecution. The principle underlying the eugenic policies adopted by Nazi Germany was that of pragmatic usefulness of human life and thus the main criterion would have been the ability to benefit society. These were also nothing new when the National Socialists were slowly coming to power, as the eugenic ideas were gathering limited popularity in Western Europe and USA since at least late 19th century.

In other words, if a person was able to lead a fruitful life despite one's disability that might have made some venues unavailable to them, government was not interfering. Even people who became disabled in combat (e.g. Great War veterans) or in the work-related accidents were being taken care by the state, usually trough benefits like injury-related pension, issued by a variety of the state agencies. Thus, what Nazis pursued, was the elimination of people unable to take care for themselves throughout their entire life and who were not only contributing to the society, but were also, in their opinion, sapping the resources that could have been used elsewhere (the upkeep cost of the congenitally ill people was a common theme in the Nazi propaganda), what extended to people with serious congenital defects. This eventually resulted in the introduction of the Law of for the Prevention of Hereditary Afflicted Offspring (ger. Gesetz zur Verhütung erbkranken Nachwuchses) that allowed the sterilization of people deemed to be suffering from serious hereditary diseases they could have passed to their children. These rulings also directly led to the murder of the patients of psychiatric hospitals who suffered from serious psychiatric conditions or mental developmental issues.

So, Joseph Goebbels, who was suffering from the clubfoot as a result of the osteomyelitis he suffered in childhood, was not likely to become a sportsman, but he was a well-educated and seemingly competent administrator and propagandist. This made him a coveted asset among the Nazis, despite his physical defect that was not getting in the way of his work.

So, to sum it up, people able to support the political efforts of the NSDAP or the state in general were not considered 'undesirable' in any way and thus were able to live and work in the Third Reich, achieving even the high governmental ranks. Conversely, Nazis were just politicians who were not above overseeing indiscretions, non-conformity or even criminal past of their colleagues (technically, Hitler himself was an ex-convict, having been jailed after the failed Munich Putsch) if they deemed the latter useful to further their goals.