It is not less secure since there's no equivalent more secure option. Don't mix problems of your network access with global decentralization. Decentralization alone is a way for better security by obscurity, but you should appreciate that whoever makes the project are volunteers having scarce resource and who don't want to make it a job for making it perfect for infinitesimal concerns.
I have no idea what "original" you refer to in this context. If the Web is more secure with broken HTTPS here and there and fully centralized access, you probably didn't fully understand what the dWeb project is doing.
And yes, the equivalent more secure option is running a website on the boring old normal internet. This solution actually gives more power to centralized operators, allowing your ISP and government to take over the connection whenever they want, a problem that doesn't exist for normal websites.
If your more secure alternative must be decentralized, then Tor hidden services are the go-to option, running on a decentralized network with actual working and battle tested security.
You can claim the problem is "infinitesimal" all you want, but until you point out a problem this solution solves that has more users being actively attacked than every person in China, I'll just assume you must be trolling.
What is the point of a decentralized solution that is less secure than the original and can be easily thwarted by more actors than the original (which we know happens to entire countries in the real world)?
Papers are distributed with IP-addresses stamped in many pdf files upon their downloading from publishers, and nobody seems discussing it. This is incomparably more harmful than some random MITM somewhere done by someone and requiring an infrastructure invasion. But even this has not yet posed a real threat.
BitTorrent: anybody directly intercepts the IP-addresses of seeders, and again, no much worry. No need to hack in as with MITM, it's just yours, go watch.
So, no problem with MITM in this project, at all. People who want to steel the projects reputation or name, simply squat domains or make various groups.
In my opinion MITM is no much different from intercepting a phone conversation by connecting to physical wires going to your apartment. It's very localized.