The 21-year-old striker was due to stay at Griffin Park until January but is now likely to be sidelined for the majority of the season.
Bees manager Uwe Rosler said: "We all wish Conor all the best.
"He did very well for us and will be a big miss, he would be welcome back at any time. He started his Brentford career in a very promising way.
"We can see how hard it will be to replace him and get someone in with his qualities and his hunger.
"It was very unfortunate and it will be good for him to be close to his friends and family for his rehabilitation."