Vladimir Putin is no doubt responsible for the death of a Russian journalist that was critical of him. Putin is known to be ruthless, and his background as a former KGB agent bears this out. It is also in-line with his personality to punish dissenters, as Russia has become more closed since he has taken over.
Although the world will never know for sure if Putin is responsible for this murder, the effect is certainly chilling regardless. I imagine that the dead bodies that surround Putin aren't just a coincidence. This makes it a risky proposition to speak out against him, which I am sure is the entire point.
Yes, Putin has a track record of silencing critics through any means necessary, from imprisonment on trumped-up charges to mafia-style executions. Any one case is hard to judge without proper forensic investigation of course. But in a case like this, we see strong motivation coupled with old-school KGB scare tactics of making an example of a dissenter, putting Putin down as a very likely instigator.
While there may be some indirect influence on the killing, to speculate about the nature of this crime--whether it was a "hit job" or not--is not something I feel comfortable doing. The only certain thing I can state is that the person who shot this Russian journalist is responsible for their crime, and they should be adequately punished for that crime.