If a creature has been dealt damage by a source with deathtouch since the last time state-based actions were checked, that creature is destroyed. The damage itself leads to the destruction.
But that's not the case for Stinkweed Imp. Its damage does not leads to the destruction, a triggered ability eventually does. It must assign damage normally, so it must assign all three of its damage to the flyer.
Here's the key difference: One can respond to Stinkweed's Imp's ability. It can even be countered.