The popular eight-year-old, who shot to prominence when taking the bet365 Gold Cup at Sandown in April, was running a storming race in racing's blue riband and enjoying himself towards the head of the field under Jordan Gainford.
In the process of belying his odds of 40-1 with a tremendous performance, the Galway Plate and American Grand National winner unfortunately came to grief two out.
"We are very proud of the horse and thanks be to God he's OK. He was going so well," said Hanlon.
"He always hits a flat spot and he was just after coming out of it, and Jordan was very convinced that, while he might not have beaten the winner, he said, 'I thought we might have been second'."
With ground conditions softer than ideal, Hanlon was in two minds about running him against Galopin Des Champs and Bravemansgame.
He added: "If only the ground was better. He needs good ground and the ground would have been too soft for him, but he gave a goodish account of himself.
"I'd say the ground hasn't been as soft for seven or eight years on the Friday.
"It was a tough decision to run. We walked the track twice - once at seven o'clock in the morning and again at 11 o'clock - and it was amazing how much it dried out between seven and eleven.
"He'd handle good ground. But in our country it would have been yielding to soft. It was tacky ground."
Hewick will be given time to overcome his exertions and while Aintree is almost certainly off the agenda, Hanlon has not ruled out bringing him back for a defence of his bet365 Gold Cup at Sandown or the Punchestown Gold Cup.
He said: "He's good now, thanks be to God. We are happy to have him home because he got an awful fall.
"He won't go to the National. I would be 99 per cent sure. We'll see how he is, but he has had such a fall. We'll probably end up going back to Punchestown for the Gold Cup.
"He'll have better ground and it's six weeks from now."
Hewick, who was purchased for a mere £800, loved the quicker conditions when taking the valuable prize at Sandown's traditional end-of-season finale last year.
While the extended three-mile Grade One Punchestown Gold Cup may be the preferred option, a return to Sandown has not ben ruled out for the gelding who has earned just shy of £400,000 for owner TJ McDonald.
"I wouldn't mind going back to the bet365 Gold Cup. I will talk to the owners and see," added Hanlon. "He'll either go for the (Punchestown) Gold Cup or the bet365 - he'll go one way or the other."
The Cheltenham Gold Cup was Hewick's first run since taking the American National at Far Hills in October and the County Carlow handler felt that while he needed the break, he may navigate another path back to Prestbury Park next season.
Hanlon added: "We will go different next year. We will probably give him a run maybe at the Dublin Festival, because he hadn't had a run for six months, which was a long time, but I'm not sorry we didn't give him a run, because he needed his break.
"Listen, we are thrilled with him and everyone got a buzz out of it. He's the people's horse, but because of the fall, the National has gone.
"He lives to fight another day and we know we have a good horse. He's entitled to be there at Cheltenham again next year to have another go."