Talgrath, for me your strategy as a gm is totally acceptable and fine. If you want that your player's characacters are _not_ highly optimized, I recommend one of the following strategies:
1. Use easier enemies than the archetype characters from the corebook. If player's sam has let us say 10 dices in his weapon pool, the probability that he wins (and kills) a gunslinger adept from the corebook, is 50%. The characters can easily die if they fight against as powerful enemies.
2. Use prime runner level characters.
I personally think that the first option is better.
Moreover, give your players more karma than the standard guidelines give. If the characters have 4 in most of his skills and 3-4 in his attributes, the progression speed is really slow if you give only ~5-6 karma per run.