How do search engines efficiently retrieve documents in a sorted (e.g. page rank) order from an already sorted (by document id) inverted index?
I don't know what search engines actually do, but one approach would be sort by decreasing pagerank, resolving ties using the document ID.  (In other words, the primary sorting key is the page rank, and the secondary sorting key is the document ID.)

This still allows the merge operation.  It also ensures that results are generated in decreasing pagerank order, i.e., the top-ranked results are generated first.  Note that if two documents have the same document ID, then they'll definitely have the same pagerank, too, which is why this approach works.