Yep, there's lots to consider when choosing and balancing weapons. The BL2 is a superb weapon though. So good you don't need missiles at all until later sectors. I'd even sell the Breach at the first shop.
Artemis + BL1 is a much more balanced combo, and it would actually require the missile weapon to be used. Ofc, it doesn't scream Desert Eagle anymore either
Maybe if you limit the weapon slots to 2, it would become a much different ship. Near invincible early on, but later you'd be in trouble without enough firepower and support weapons. And no teleport or drones means you would need 2 VERY handsome weapons to win.
Here's one more suggestion. Instead of a missile, create a bomb weapon similar to the breach missile. Bombs are unstoppable by defense drones. Only a suggestion though.