I know that Saiunkoku Monogatari is based on a series of light novels. How closely does the anime (both seasons) follow the original series? What are its main points of deviation?
Are there differences between the novels and the anime?
In a word, yes. I try to note these in the summaries. In the first season, the differences are relatively minor. Some minor subplots have been eliminated, or switched around, and some scenes added or subtracted. In the second season, although the major events and plotlines remain the same, some of the foreshadowing for later events has been cut. For this reason, I advise you to read the summaries from volume 9-10 on, if you are interested in understanding the post anime events. I have also tried to do translations of scenes that were altered or entirely cut from the anime which change our understanding of the characters and political situation.