Ultimately, you can do anything you want. :P

I think it's a particularly nuanced issue and part of the problem in giving any advice is that you are speaking in generalities rather than specifics. Being a History major I get squeamish when people go mucking about in facts. A different interpretation to the facts is certainly acceptable. As all my professors say, "I don't care if you disagree with my assessment of the facts; just make a case for yours." There is also an incredible amount of history (especially very old history) that people regard as completely factual when it is actually considerably more nebulous.

So if you aren’t changing anything that is largely regarded as factual, then it’s completely fine. Perspectives and shades of gray can get twisted, especially for good fiction. Even changing minor facts and aspects of the events is acceptable in my opinion as long as it is relevant to the story. Don’t change things that don’t need changing.

An example I can give you that I did for a project I’m working on is related to certain historical discoveries. In this work of fiction, Phoenician has never been translated in any great detail and instead is kept alive solely by a select group and used as their private language. In truth it has never been fully worked out or deciphered (to the best of my knowledge, I’m not always up to date on current discoveries) but it has been given quite extensive work and as such is far more translatable than I give it credit. Is that correct? No. Not really, but it works for the story.

Whatever works for you works. You’ll also never make everyone happy. No matter what you do, some will be angry because you deviated from history a little. Others will be annoyed that you didn’t take more creative license. Just do what you think is best and it’ll either work out, or it won’t. Good luck.

- Geoff