It's a good, valid question and the article is also a very good read!
It does have a point. It would appear that blockchain defeats the purpose of what GDPR is trying to accomplish but I believe everything is on the way you implement things.
For example: If I decide to integrate my ERP with any blockchain, would I need to have people's data in the blockchain? I don't think it has to be that way; not everything has to be "blockchained". What I would do is assign an ID number to that particular person, keep their data off-chain and everything else in the blockchain. When a person wishes to exercise their right to be forgotten, my ERP could very well get rid of their personal, identifiable data, and only a number would still be attached to everything else regarding, say, number of purchases, which items per purchase or per visit to the website, etc. without specifically identifying the person.
Governments have a lot to do when it comes to regulation and overall handling of blockchain technology but I believe it's the ones who are starting to build things who must be very creative in their ways of implementing such changes in order not to shoot themselves in the foot; nobody want to be in non-compliance, but everybody's in for the hype! I, for one, think there's room for both.
