This lock seems unnecessary (and causes deadlocks), and at least should be acquired at a lower level if it's needed.

I think this is here from when noop and index build oplog entry application were together and index builds needed this lock (https://github.com/mongodb/mongo/commit/188fcbc3bf1ad7ff7f8114c33412fd9e27295c79). When those two code paths were separated noops inherited this lock as well to be safe.