There is absolutely no doubt that halogenated hydrocarbons such as Halon have a destructive effect on the ozone layer, that is basic chemistry.
However the amount released by aircraft extinguishing systems is so miniscule and so rarely released that I cannot see how it would have any real effect.
Also I'm sure a crashed aircraft due to an uncontained fire due to no Halon suppressant system would have a fair more detrimental effect on the environment than the alternative.......