Well, more specifically, Poisonproof A++ cures all poison effects and heals. That's literally the dedicated effect. Pain Breaker also cures all debuffs, heals, and applies debuff resistance, which includes poison resistance. If those aren't good enough to mitigate Hydra venom to being non-lethal, no one in this entire story who has been affected by Hydra venom should have lived, "glancing" hits or not. Immortals typically don't even die specifically to the venom, they just don't heal from it, then go insane and die in some other fashion.
If Medea Lily can't cure Hydra venom, Hydra venom is more powerful than Hassan of Serenity (admittedy, Semiramis is older, so should have some advantages as far as Mystery goes), and probably can affect Olga Marie while she has Mash summoned. If Hydra venom is that effective, it should be listed specifically as a Noble Phantasm. As it is, Sikera Usum, which is a specific application of possibly Hydra venom, is B+ rank and explicitly notes that it's heavily weakened against people with legends of poison resistance, though it gains a conceptual bonus against people who are defeated by poison in their legends.
Medea Lily is the nuclear option when it comes to countering poison. You don't ask "can she cure the poison?", you ask "how can I prevent Medea Lily from getting in a position to cure the poison?" or "why does this not actually count as poison", just like you don't ask "Is this powerful enough to penetrate Avalon", you ask "how do I get Avalon away from Saber" or "how does this effect specifically counter Avalon's interdimensional dodge" (for example, I can see an argument that Rhogomyniad, specifically, might counter Avalon's activated effect). Her poison countering is incredibly specific, and specific beats general, conceptually, when it applies, barring overwhelming power difference.
Hydra venom is not Ea, it doesn't just go "screw the rules". If Gilgamesh has super-ultra-original venom from the serpent who stole his immortality potion, that forms the mythological basis for the Hydra, sure, whatever. But if you show that something can be survived for some time, and cured over time from modest exposure, and resisted by divine protections, saying the most specific counter to it is insufficient seems ridiculous.