I heard an interview with him on CBC's As It Happens a few weeks ago. He basically said "Of course I'll be found guilty. Putin owns everyone. Judge, prosecutor, defence, everyone." He knew he'd be found guilty - and this is the second time that this has happened to him. Same charges and everything: I guess embezzlement is easy to make stick and is bad for the reputation.
I'm not sure how bad it is for Navalny's reputation. I expect that most of his supporters are entirely willing to accept that the charges are trumped-up/false (which seems plausible to me, in fairness). They may impact his chances of actually winning the election (provided the election is a fair one to begin with) if he is able to run in the end. But for now, I'm not sure that this ruling is going to change much in terms of Navalny's reputation. Also, funnily enough, I posted this just before Existentialist: