1. Everyone who opposes Putin dies or ends up in jail.
2. Putin hasn't been tried in court to be proven guilty, so we don't "know" who's responsible.
2 is actually barely relevant in context. The fact of the matter is that the chilling effect occurs regardless.
That the incentives clearly points to one explanation and nothing else makes sense is unmistakable, but also secondary.
a) Not everyone - a lot of people oppose Putin. https://echo.msk.ru, https://novayagazeta.ru Most content on these sites devoted to critisizing Putin and current regime. These people do this for years.
b) Not everyone from your list opposed Putin, for instnace Khlebnikov mostly concentrated on Beresovsky.
2. Correct. We don't have any official evidence. This means that the only thing we can do is to analyze what is available. The links you provided don't help much in this endevour.
We know that people die or are jailed. We can definitely see patterns that group those people together. Everything points to a single explanation, but regardless if that is proved or not, the effects are black on white.
I don't have to understand/prove weak forces or gravity to state that 100 of 100 apples dropped fall to the ground.
Black and white facts are the person murdered, crime commited and some other person guilty. The hypothesis is who this other person is.
The fact that the person murdered is not the most dangerous for the person suspected support the hypothesis that this has been done to discredit him. (but doesn't prove or disprove the hypothesis).
The fact that nobody has been prosecuted supports the hypothesis that the suspect is guilty.