@Oh GOsh these guys actually grenaded me inside my ship!
I think you take the Bonaventura for what it most certainly isn't: a defensive bunker. It was designed as a 100% offensive craft and ought be used as one. Enemies in front of you should be immediately killed, if that proves impossible, smoke the inside and disperse. And pray. Well, it's a hazardous job. On the other hand, it offers you best chance to quickly dispatch enemies around you; that was the source of my greviance with "no explosives until turn 3" mode, since by turn 3, oftentimes I've managed to kill more than half of the enemies on the map and cause panic amongst the rest. I can't put a door on the back end of Bonaventura, since the opening is 2x2 for ease of throwing grenades outside & possibility of shooting from the perch. If I put a door there, I'd have to wall the upper half of the opening. Plus the annoying TU loss to open the door, you might need these 6 TUs for offense
If you want a defensive craft, sell the Bonaventura and buy a Pachyderm. Or wait until more advanced craft are available (Deliverator is fairly easy to develop, and it's also fairly defensive).
@Cattle prods
Sell the stun rods, buy cattle prods. Stun rods are left so the guys who still own them can sell them for a full price. To anybody else, they're invisible and unobtainable. They still work if you really want to use them, but they're weaker. And, the main reason why Cattle Prods were introduced: it is possible to put a melee hit sound on them, while it is seemingly impossible with stun rods for some reason.