I want to chime in to offer the counter. I used to work for Gemalto. I'm not exactly sure which keys you are talking about, but when I was there Gemalto's standard practice for the transfer of the keys mentioned in the article--individual SIM embedded keys--was to use AllynisConnect (which I only mention because it's easily found on Google) to facilitate the transfer of individual SIM keys to the customer. Obviously I'm not going to comment on the details of the cryptography involved, but it was much more considered than "simple encryption methods or no encryption at all."
Notably this mechanism would not protect the keys against an attacker who was inside Gemalto's or the customer's secure network, as seems to be the case here.
I'd be interested in knowing which keys specifically you are talking about.