Yes, but those ports are still an important strategic and economic asset to the country.
A lot of harm could be done and a lot of confusion caused just by screwing up the business side of things.
Since this company isn't going to be able to just replace the current employees it would be very difficult for them to screw things up on purpose without it being noticed very quickly, but does seem to still be a significant risk to allowing a company owned by the monarch of the UAE to run the business of these ports.
Not to mention that this little shibboleth (that terminal operators have no role in security) is patently false. I'm not sure who started spreading this ridiculous story, but it's a pretty brazen misrepresentation.
They're not putting the fox in charge of the hen house, but they are giving him an office in the hen house...