I can't understand why this has suddenly become an issue. Akismet has always been a commercial service, they've just adjusted the point at which you need to start paying, that's all.

The simple solution would be to just remove it from core. It's still an excellent plugin. The only problem I see is that it's pimping a commercial service in the core software, which has always felt a little odd, but that's not a recent change, it's been like that ever since it was integrated into core many years ago.

I noticed the TOS has been adjusted a while ago, and have slowly been taking Akismet off my sites one by one. I've actually seen a reduction in span since doing that, as the new tools I implemented were more effective at blocking spam than Akismet ever was.