The 37-year-old suffered serious neck injuries, fracturing his C3 and C4 vertebrae, and is being treated at Frenchay Hospital in Bristol.
Geraghty said: "I just wish it were a happier day, because we are all upset about John Thomas.
"You have to put it out of your mind when you're racing but, even though this is one of the biggest days of my career, all I could think about was John Thomas. He's a friend of ours and I hope and pray he will be OK.
"When you are out there, you are doing a job. When you finish, it comes straight to you in a moment like that. It was bittersweet."
JT, or John Thomas, McNamara is a leading Irish amateur rider who has been a winner four times at the Cheltenham Festival, including guiding Teaforthree to victory in the National Hunt Chase last year.
He won the same race in 2002 on Rith Dubh, was successful in the Cross-Country Chase with Spot Thedifference three years later and won the 2007 Fox Hunter Chase on Drombeag.
Geraghty and his brother Ross bought Bobs Worth as a yearling for 16,500 euros (£14,275) and sold him to Henderson as a four-year-old for £20,000.
The eight-year-old, in only his sixth race over fences, won at Cheltenham for the fifth time in his career and secured a third successive Festival triumph after victories in the Albert Bartlett Novices' Hurdle and RSA Chase.
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