There are also improvements upon Kademlia such as S/Kademlia which we've partially applied to IPFS (and we'll continue to apply more).
Splitting routing into peer routing and content routing isn't going to fix this if you're still using a DHT to do both. Also, S/Kademlia's decentralized countermeasures only slow down the attacker, and they don't save you if the attacker has a botnet.
> We're planning ahead for future mitigations by making every layer of IPFS pluggable.
The problem with this line of thinking is that it ignores the fact that IPFS-with-DHT-routing is a fundamentally different system than e.g. IPFS-with-DNS-routing, which are both fundamentally different from IPFS-with-Namecoin-routing. This is because they each make fundamentally different guarantees about availability, durability, and security. In general, the end-to-end properties of a distributed system do not logically decompose.
Plugins make this problem worse, not better. Now it's not enough to know that I'm storing my data with IPFS; now I also need to know which plugins both I and my peers are using using since the set of plugins is what determines the properties of the data store.