2. there comes a time when the cup of endurance runs over, and men are no longer willing to be plunged into an abyss of injustice where they experience the bleakness of corroding despair.

is an example of a metaphor

that means that there will come a time where men will run out and lose their endurance and can no longer deal with injustice, which can give them the feeling of despair

tone:

urgent mood:

3. to a degree academic freedom is a reality today because socrates practiced civil disobedience.

socrates disobeyed laws that were not fair, which made it so students today can think freely (and possibly differently than their teachers).

tone:
thought-provoking mood:

2. There comes a time when the cup of endurance runs over, and men are no longer willing to be plunged into an abyss of injustice where they experience the bleakness of corroding despair. 

Is an example of a metaphor 

That means that there will come a time where men will run out and lose their endurance and can no longer deal with injustice, which can give them the feeling of despair

tone: condescending

Urgent mood: despair

3. To a degree academic freedom is a reality today because Socrates practiced civil disobedience.

Socrates disobeyed laws that were not fair, which made it so students today can think freely (and possibly differently than their teachers). 

tone: freedom of thought
Thought-provoking mood: academic freedom for students