Although Putin is a suspect, I would expect there are many other powerful people who wanted Prigozhin dead. If Putin wanted him dead, I think he could have easily arrested Prigozhin when he refused to integrate Wagner. Waiting two months doesn't seem like the way to make "the biggest" example of him. But I am no Russia and/or Putin expert.
I would think that both unnamed Russian oligarch(s) backers of Prigozhin's Putsch attempt, or CIA could be behind it. If either group was involved in the coup, eliminating a possible leak is reason enough. The CIA can never be ruled out, for multiple other reasons.
It would be interesting to read your take on the above.