Pirenne's thesis is interesting, and that it polarize for or against it shows how much it's important for the early-to-classical medieval history.
Of course, his main points are to be nuanced in the light of new archeological and scientific evidences, but I find them to hold rather well. Let's say that when Pirenne lacked substance (and it was far from being a common occurence), he had intuition.
A good complementary study (or even a basic one), for what matter the development of towns and trade in North Sea would be Dark Ages Economics, by Richard Hodges (if possible, in its edition of 2012) which owes a lot to Colin Renfrew's take on historical development, mixed with an aggiornamento on Pirenne. It's clearly a scholarly book, altough the author knows how to make itself clear, and introduce the basic theories fairly well.
Pirenne's work is, a bit like Bloch's, to be nuanced with the new evidences, analysis and methodology, but remains more than just historiographical testimonies; so for one, I wouldn't crucify anyone on these.