IPSec by itself isn't going to really help. If they are doing DPI, they can MITM your IPSec connections. You still need a key management system, and I am not aware of any large-scale systems that are in-place to just "switch on" IPSec, that is, suddenly provide you with the certificates for every IP you want to connect to.
You're right, it could be a passive inspection. But... if they are your ISP and have access to your packets, chances are they can rewrite and inject traffic too. Sure, they might need a bit more hardware to do so, but it's not exactly difficult.
But you're correct, DPI doesn't necessarily imply MITM capabilities.