Is there any way to avoid merge commits? It kind of defeats the purpose of letting main move fast if every change creates the ladder structure (see image). I tried disabling merge commits in the github settings for the repo, but then merging on Graphite fails.

When you click the merge button in Graphite, there should be a modal that pops up that allows you to pick what "Merge strategy" to use. If you want to avoid merge commits, then you want to change this away from "Merge pull request" to either "Squash and merge" or "Rebase and merge". Also, in the "General" GitHub settings for the repo, you should be able to uncheck "Allow merge commits" for the repository, if this option is not checked, Graphite will not provide the option to use the merge strategy.