Shirer's The Rise and Fall of the Third Reich covers this area pretty well (and covers A LOT of Nazi Germany's early day really well). Sadly I no longer have my copy so I can't cite the specific chapter, but essentially he states that Hitler was well aware of Rohm's homosexuality more or less from the get-go.

Hitler doesn't seem to consider it an insurmountable obstacle as long as it wasn't general knowledge. More like any vice/addiction that needed to be kept downplayed like alcoholism, gambling, etc. I believe Hitler even stated in a rebuttal to one of his inner circle, after he raised the problematic nature of Rohm's sexuality, that the SA were his stalwart enforcers, not moral compasses, or something to that effect.

Hitler held off having Rohm killed for as long as he could, but when he finally did it was for political reasons and certainly not because of his sexuality. That being said, this didn't stop Hitler's PR people from labelling him as a pervert after his outing.

As to why or how Hitler justified having a close friend as a homosexual but had others murdered, we can only assume how he personally reconciled these. More likely than not, Hitler didn't like homosexuals, and used it as well as other descriptors to justify the extermination of "undesirables".

EDIT: It's important to remember Shirer's work (and therefore a lot of his language and perceptions) are quite dated, being initially published in the early 60's by a generally conservative author. But it remains a solid primary source that is commonly referenced and cited when it comes to the rise of the Nazi state and internal politics in the third reich. Shirer was not, as some commentors have accurately pointed out, a historian or a scholar in a strict sense. But that does discount the validity of his work or relevance in examining these kinds of questions.