I willl probably get some backlash for this, but I think thrusters could work similarly to radiators when it comes to heat propagation. So, even if your ship has a thruster placed entirely inside it while respecting the thrusters dead zones, you would still need to account for the heat it generates.
To allow players to place thrusters inside their ships, there could be a new "armor" piece called the Heat Absorber. It would have zero armor value and include an internal two-pipe connection. Any heat it receives could be redirected into pipes, either to be expelled by radiators or repurposed in some other way.