This is actually quite a controversial change mainly because of their switch to a CLA. This indirectly gives them the opportunity to switch the license to closed source whenever they feel like it in the future. Semi-controversially, they are also primarly making this AGPL change in order to begin selling dual-licensing to companies. The Matrix Foundation itself does not support this change from Element, though Element is within its rights to do so.
You can read some more thoughts on this from the pessimistic folks at HackerNews. My main takeaway is that I don't trust Element because I don't trust anyone. I'm sure they're doing this in good faith but I don't like the power they have at the moment. I hope this is what's needed to begin focusing efforts on alternative homeserver implementations like Conduit.