So, first of all: your way of ruling it is totally great, if that worked for your group!
When I have a poisoner at the table, I always remind them to create some poison, even if they don't have a specific purpose for it just yet, during every planning scene, including the initial, free planning scene at the start of the Job. That way, they always have something in their pocket.
In situations where the player doesn't have the thing that they need at the moment they need it, I always fall back on Influence as the way for them to get it. If they don't have any Influence, and they haven't created a poison during a planning scene...well, sometimes the fun of the heist genre is not having the tools you need at the moment you need them, and improvising! I might have allowed the player to whip up an improvised poison during the scene, letting them narrate combining certain liquors and other, possibly illicit substances they stole from behind the bar. In such a case, interesting tension could come from needing other players to nick the ingredients without the bar staff being made aware, or mixing up a concoction in the middle of a public place without being noticed. I can just see in my mind the poisoner huddled off in a booth, trying to quickly whip up a poison without being spotted by the other patrons walking by! Having them create the poison in-scene is a great way for them to do their schtick, and get a die roll out of them...and die rolls are where heat, complications, and other drawbacks come into the game, making things more interesting.
As for using poisons against enemies, at the end of the day you can treat it just like any other attack, using the poisoner's skill just like you would use any other skill to attack. If the player managed to poison a whole squad of minions, I'd give them some advantage dice (see the "Attacks that Should Hit Multiple Minions" sidebar in the Judge Rulebook) so they can take out many members of the squad. Otherwise, their roll would just deal damage to a character with luck as normal. I'd be liberal with advantage dice if the players' creativity led them to create a poison that should be particularly effective.