It is always a mistake, in my opinion, to try and judge events of so long ago in the light of today. In 399 BC Athens was only just beginning to recover from the loss of the Peloponnesian war (against Sparta and her allies). Athens had been utterly defeated, her walls had been torn down and the victors had imposed an autocracy on what was a Democracy until 404BC. Athens had also lost her empire and the revenues that flowed from it.
Was the Athenian Democracy perfect? No, but it was a noble experiment for all that. I think it is not unreasonable to consider all the circumstances of the trial of Socrates in the light of the the political situation at the time. What would have been the fate, for example, of somebody in the newly created United States (just after the revolution) who preached return of the King and the abandonment of Republic?
Or, perhaps more allegorically, to someone in the British North American Colonies (i.e. Canada) who proposed the overthrow of rule from London in favour of a Republic?
I should hasten to add that I have not had time, yet, to look at the link in the OP. I will do so, though, with great interest.
And yes, Thucydides book of the Pelopennesian War is one of my favourite ancient texts.