Not sure if this kind of question is allowed but since I have to write a paper about Custer I want to get a sense of how historians keep personal morals in mind. Pretty much everything he did in the Indian Wars would be considered war crimes by today's standards but he was lauded. Do we keep analysis relative to the values of the time?
More broadly is this an issue in academic history?
Great question! I worked with Silvio Manno as he crafted his masterwork Charcoal and Blood: Italian Immigrants in Eureka, Nevada, and the Fish Creek Massacre. Silvio felt passionately about the terrible exploitation - and then murder - of his fellow countrymen. He did a wonderful job laying out the facts, but I felt that his passion too often erupted into judgment throughout the text. I cautioned him to simply tell the story - which was dreadful enough in its own terms, and to keep the judgement to the conclusion and to other discrete spots in his essay. He didn't need to hit the reader over the head by pointing out how terribly the Italian immigrants were treated - the story made that clear without additional moralistic writing. That sort of restraint can be difficult with some subjects.
I can't imagine writing about Custer - or Hitler or anyone like these sorts of characters from the past (or their counterparts today!) - without spurting all sorts of words to condemn them and their acts, repeatedly and throughout the text. But history is best when it doesn't read like a sermon. Tell the story, and save the sermonizing for discrete locations. That was my advice to Silvio and it is what I suggest to you.
In addition, as you suggest, it is important to be careful when we impose modern standards on the past. Custer should be judged by modern standards, so it is clear that we can't approve of what he did, but we must separate that judgment from what he did that was right or wrong in the context of his time. He was a terrible general - and that's a judgment worth making for his time. He was a war criminal - and that is a judgment that we must impose on him from the present.
There have been several threads in the past, including a roundtable discussion, about the concept of [presentism](https://en.wikipedia.org/wiki/Presentism_(literary_and_historical_analysis)).