So, two options: Either there is some sort of ritualistic "coming of age" thing, which means that the entire population or nearly the entire population has acquired tolerance to the toxic compounds in kresh. Or then there has been a chance mutation in the population, resulting in a subpopulation that is naturally tolerant of the compound. Since the population levels assumably collapsed during the fall, it may be simple chance that the tolerant population was left.
And notably, the Caldari are not immune to the poison, only tolerant. Now, if including player fiction, Caldari can drink hak'len and live where Gallente will have death due to suffocation. An alcoholic drink is notable, since alcohol is also having a mild depressive effect (to the point that mixing alcohol and morphine may be fatal due to depressing the central nervous system).
Then, there is the kress tea, which reminds me of pufferfish/fugu: A kind of a delicacy (well, Caldari use it ritualistically) which, when correctly prepared, is safe. When incorrectly prepared, it is fatal. I would therefore assume that the Tea Makers know how to make kresh tea without extracting the toxin or, alternatively, in such a way that the toxin is extracted. It may be even as simple as a combination of solvent (water) temperature, duration of brewing the infusion, or a combination. Of course, a catalyst may be involved, as well, or the toxic compound may even break up at high enough temperatures. This would allow the tea maker to prepare seemingly similar cups of tea, possibly even from the same pot (if the ritual involves intermediate heating or cooling of the tea), some of the cups which are safe to drink and others fatal. If the water is changed, then there's one more parameter, as the tea maker can select the initial temperature of the water used, further obfuscating the water temperature from the participants. (Otherwise a knowledgeable drinker might be able to deduce water temperature from the duration and intensity of the heating, specially with a less experienced tea maker.)
Of course, at times the fate of the drinker may still be up to chance, depending on the exact concentration of the poison in the tea and the tolerance of the individual. If we assume that the Tea Maker ceremony was developed in the Raata period, then a tolerance to the poison would be a very desirable property with possibly considerable evolutionary pressure to develop. Culturally, it might be seen as the spirits favouring a specific noble who had been able to drink the tea several times (in a ceremony, not the "safe" tea served in funerals and similar rituals) without dying. Of course, assuming the Tea Maker is not impartial, this could be manipulated to make someone seem to be able to drink the Tea without dying, while it was actually safe - which could then make them more eager to use the method for solving disputes, making the person - or in case of inheritable property, his children - easier to get rid of. If noble houses select marriages based on the property, this could be one way of sabotaging their genome, depending on how the genotype manifests. Make a deal with a minor noble family with weak tolerance to suddenly appear to have caught the beneficial mutation, have one of them married off to a competitor (and thus elevating them in status) and then make a blow against your intended target generation later.