Sounds a bit to me like part of a FUD campaign or at least bluster to scare off people from seeking out tools that help protect privacy. But it does highlight a need for these tools to become more ubiquitous.
1. configure your browser to use a separate CA store from the OS one;
2. set up a VPN tunnel to a jumping-off-point not within your ISP's reach;
3. hide that tunnel's traffic steganographically within a regular "encrypted but actually MITMed" connection to your VPN server.
These three steps could even be put together into a little middlebox to put between your home router and the Internet, so each device could keep its OS-level CA store sane, while still appearing to the ISP that everything is regular MITM-able traffic.