I don't think it's possible for FreeIPA to operate on bind flat files
but I'll leave that to others who know better to answer.
I know you said you'd rather not spin up additional DNS servers but I
really think that's your best option. Build additional bind servers
that are slaves of FreeIPA and have FreeIPA act a a hidden DNS master.
If there's a problem with the DNS service on FreeIPA your slaves will
continue to handle all requests. Just my two cents, attempting to
change the way FreeIPA functions in order to improve availability may
have the opposite result.