Ugh. First, how you explain DNS makes it hella confusing. I've read it like 3x and I still don't get how it works based on your explanation of it. Also, this is just how DNS works. Everyone can redirect if they want to. Every country does for various reasons. That's not really the important bits. The important bits are whether they actually do or not and for what purpose. Moreover, DNS is not bound to a simple suffix. I live in the US and have domains that range from .ca to .us. to whatever. Some countries control certain aspects, but there really isn't any formal authority that says if you live in the US you can't have a .ca. There's so much more going on there and it's almost unenforceable at this point.
Second, yandex.ru is not a thing. Go visit it. The correct address is yandex.com. Third, a redirect is obvious and no one is rebuilding a pirate site with a redirect. You'll notice. Contrary to tinfoil hatters, governments aren't building complicated honey pots when all they have to do is sit on a torrent and fire off automated emails to your ISP. Moreover, 99% of ISPs don't give a shit and just do what's legally required of them but to this date, none have really taken action.
Lastly, your tl;dr was enough but doesn't actually speak to safety, just that "they can". The CIA can just bust in your home rn and take you to a black site, make up some shit and you're gone forever. If they wanted to. They don't because why?
Honestly, this place is so full of doomsday preppers that if someone asked if it was safe to jaywalk, they'd be coming out the woodwork like "nah man, a cop could just run you over and blah blah blah." Please.
tl;dr: yes .ru sites are just as safe as any other website