A team of UK-based volunteers prepared her body, packed it in dry ice and transported it to the Cryonics Institute in Michigan, one of just three such facilities in the world. The others are in Arizona and the outskirts of Moscow.
Speaking to the Telegraph, Mr Kowalski said the cryogenic process would damage the brain, and could wipe memories completely.
He said: "The question is whether we are saving the person's identity or their mind. Everything in between is a degree.
"The analogy would be a stroke. Most people that have strokes are happy to be alive. Some people have big strokes, some have small strokes. You won't have 100 per cent of your mind."
"You could be just like you but without your memory, without the same mind. Like a clone of you."
The parents of the girl - identified only as JS - had disagreed over whether her wish to be frozen should be followed, so she asked a High Court judge to intervene.
In a heartbreaking letter to the court, she said: "I don't want to die but I know I am going to...I want to live longer...I want to have this chance."
The girl asked Mr Justice Peter Jackson to rule that her mother, who supported her desire to be cryogenically preserved, should be the only person allowed to make decisions about the disposal of her body. Her wish was granted.
Without commenting on the specifics of the case, Mr Kowalski said: "How can you deny a dying girl's last wish and take away her last hope?"
But he added that most of the institute's patients have made their wishes known far in advance.
"We have to be careful in those situations because we don't want to position ourselves to take advantage. Some people argue that they're desperate and they have no other option, and that they have everything to gain and nothing to lose," he said.
The scientific community is divided over whether cryonics, which was pioneered by Dr Robert Ettinger, the institute's founder and - as of 2011 - one of its patients, will actually work.
After the decision emerged, experts said cryogenic companies were irresponsible for implying there is a realistic hope that a dead human could be unfrozen, brought back to life and cured of a fatal disease in the future.
They said the High Court had made "no assessment of the plausibility of the science" and warned the ruling could encourage vulnerable people to pursue unrealistic hopes.
Clive Coen, Professor of Neuroscience at King's College London, said: "Irreversible damage is caused during the process of taking the mammalian brain into sub-zero temperatures. The wishful thinking engendered by cryogenics companies is irresponsible."
Mr Kowalski admitted that he is a "50-50 guy" on whether his patients will ever live again.
"Some of our members think it's just a one per cent chance but worth a shot. Some think it's definitely going to happen. I'm kind of in the middle," he said.
"It's hard to believe we wouldn't be able to do it in 100 years. Now, a tornado could hit before then, or the government could regulate us out of existence, but the science will be there."
Ninety-three of the Institute's dues-paying members are British, the highest proportion from any country outside of the US. Before JS arrived, at least 15 Britons were already suspended in the institute's fibreglass tanks according to Andy Zawacki, the chief operating officer.
Mr Zawacki led the Telegraph on a tour of the facility, tucked into a bleak industrial complex in a neglected suburb of Detroit.
From the drab exterior, one would never guess that 270 once-living things were suspended in liquid nitrogen awaiting rebirth.
The institute, which will reach its current capacity within five years, currently holds 145 humans and a menagerie of 125 pets, including cats, dogs and birds.
A chance for new life is not as expensive as one might guess. Members can contribute $120 annually to reserve their spot, and pay $28,000 (£23,000) to be frozen, most of which can be covered through a life insurance policy. Those fees include the costs of re-animation.
The institute is a non-profit, and only two staff members are paid.
Joseph Kowalsky, who sits on the institute's board of directors and has no relation to Mr Kowalski, said JS's case had made him think of his grandmother, who fled the Holocaust and arrived in the US at age 14.
He said JS would have a similar integration process if revived in some distant decade.
"My grandmother didn't know the language, she lost most of her family, the technology in the US was like magic to her, but nobody would have told her, 'why didn't you stay behind?"
