re: Are our naval forces prepared for this?

When you mention supersonic missiles, I think you mean hypersonic missiles. It is these hypersonic missiles that US Harpoon missiles compare unfavorably to.

Your link is to an article about anti-ship ballistic missiles. These are the so-called "carrier killer" missiles. As they are ballistic missiles, they fly to very high altitudes and follow a ballistic trajectory. This is really a completely different creature than a normal anti-ship missile like the Harpoon.

Ballistic missiles have generally been used to hit fixed targets. Targeting and hitting a moving carrier, which despite its size is a speck in the ocean, with a ballistic missile is no easy task. Anti-ship ballistic missiles could turn out to be worthless or they could make super carriers obsolete.