There might be difference in performance for administrative operations (e.g. resharding), but they should all be positive changes!
EDIT: Daniel beat me to it.
Note that in the beta, reconfiguring tables over servers on rotational disks can be slow https://github.com/rethinkdb/rethinkdb/issues/4279 . If you store large documents, you might also see some increases in memory usage during backfills https://github.com/rethinkdb/rethinkdb/issues/4474 . We're going to address both of these issues before the final release.
So, you've made the noob mistake in using Raft, where only configuration goes in the log and actual changes to data aren't replicated in the same manner.
This allows us to provide different degrees of consistency guarantees for the data, depending on the user's need. Our default is already pretty conservative, but allows uncommitted data to be visible by reads. In the strongest consistency mode, RethinkDB 2.1 provides full linearizability (see http://docs.rethinkdb.com/2.1/docs/consistency/ for details). We have confirmed this both theoretically as well as by testing the overall system using the Jepsen test framework.
If you're looking for different degrees of consistency, I'm fairly sure you can do that without protocol level changes to Raft.