Honestly, if you're a man Flynn's age, you can survive a couple of years in rich-people-prison (or just: prison, for readers from the civilized world). It is safe and dry and there's food to eat. He was in the military for decades, participated in the invasion of Grenada and served in Haiti. He has seen worse places.Flynn's son? Someone fill me in if the answer is yes, I didn't know about this. But even if you're right, can't Trump just pardon his son too?
His son is still young with a career ahead of him. Prison will hurt, and a conviction for espionage doesn't look to good on your resume even if you're pardoned.
So I can see why Flynn would take a fall for his son.