If we're not going to scrap the new poison system altogether, my suggested tweaks (for the moment) would be something like Assassins getting something like a +2 or x2 level bonus when casting APHEELSIK (which would be consistent with Warlords and Paladins being better with their own glyphs) and having the dagger and TT boon add more poison when you deal more damage (e.g. hit for 5, add 5 poison, hit for 25, add 25 poison; or whatever numbers are suitable).
Regarding APHEELSIK, Assassins aren't the only ones with problems. The glyph itself will need substantial buffing if it remains like this. Furthermore, it's functionally useless for low-level characters. Because it's so mana-intensive now, pretty much all of the glyph combos that used to work (if you were willing to sink the tiles into doing so...) are now dead. I'd say something like 100+20/level stacks is the right way to go.
I considered suggesting exactly what you were talking about in terms of connecting poison stacks to damage, but I realized this would be double-dipping since high attack-damage is already preferable for these kinds of characters. I'd say make it 2-3 stacks per level, and then migrate the poison boon to a 25+25 piety cost with 10 gold.
I think this change really opens up the comparison of the venom dagger / poison boon with the vampiric blade / blood hunger boon. Moving over to a per-level effect, similar as was done with lifesteal, sounds like the right way to go here.