I found a clip on YouTube (via an article on Jalopnik) of an Aer Lingus pilot departing from JFK. Due to a weather cell showing up on his instruments, he can not make the left ATC asks him to make.
ATC advises him that the weather is not as bad as the pilot makes it out to be.
ATC: "Shamrock 104 heavy, it's light. I have 6 categories of weather here, it's the lightest category. I've had no adverse ride reports south of the airport by 10 miles."
He then is put in a holding pattern (while departing) until the situation is resolved. He is then told that the last 6 craft departing had no problem following that heading.
ATC: "Shamrock 104 heavy, you're gonna go the way the last 6 GREKIs went while you did this overhead Kennedy."
Was ATC overstepping its boundaries advising a pilot to ignore a weather warning?