Antifungals will kill the fungi species in the candida. Some antifungals are also broad spectrum antimicrobials (e.g. olive leaf or oregano oil) and will kill some of the bacteria too. However, killing off the candida is a good idea if you can manage it. If you are taking antifungals while taking kefir, I would imagine you are killing good and bad (candida and kefir) at the same time, but constantly repleneshing good (by drinking more kefir), so you should end up with more good than bad. Seems like a good strategy. But in practice, I have not tried it so couldn't comment on efficacy.
However, I have never had any success with antifungals in trying to combat my candida. How are you doing and what are you using?