I strongly prefer a rebasing workflow to a workflow that leaves merge commits, if that’s what you mean.

Merge commits have a special meaning — they are exactly commits with two parents. That means that if you have a merge commit, your commits no longer form a tree. Some tools like rebase and bisect work badly over merge commits…and 9.5 times out of 10, there is no good reason to have merge commits, as the other parent represents a commit ID that is both uninteresting, and lives nowhere else.