Bigirimana, who arrived in January, has yet to feature for Gers after being diagnosed with a mystery illness.
"Bigi has got a medical condition which is a personal matter," said McCall. "The doctor and consultant are all involved in that.
"I knew him at Coventry. I remember watching him and thought when I came into the job he will be a good one to bring in and give us a bit of energy. Unfortunately because of his medical condition he won't be able to play for us.
"But that is as big a blow to the kid as it is for us. It's not his fault, this [row] has been nothing to do with him. He comes in with a smile on his face each morning, he trains with the fitness coach as hard as he possibly can.
"So as disappointed as we are that we can't use him, you have to think of the boy in this matter because he can't go back, he can't play for anyone else.
"It's an unfortunate circumstance that really should never have happened."