Relative to each other...:
The Afuris have a lower base damage (14), firing rate (20.0), and reload speed (2.7 s), but also have a greater magazine size (70 rounds). The Afuris would most likely benefit from damage, reload speed, and fire rate mods.
The Twin Vipers have a lower magazine size (28 rounds) and reload speed (1.9 s), but also have a higher base damage (16) and firing rate (25.0). The Twin Vipers would greatly benefit from magazine size mods and probably reload speed ones as well (to offset the reload times).
Both of these weapons have the same accuracy (8.7), max ammo capacity (210), and critical damage multiplier values (150%). Plus, as you stated, both have a terrible rate of ammunition efficiency. They do have some armor penetration issues though, so keep that in mind.
Overall, the Twin Vipers have a greater base max damage potential (3,360) compared to the Afuris (2,940). Yet, the Afuris have a greater base damage per magazine (980) compared to the Twin Vipers (448). You'll be burning through each magazine on the Vipers much faster, necessitating more reloads. Do you need sustained and quick (burst) damage? Go for the Afuris. If you need long-term damage, go for the Twin Vipers. Personally, I say choose the Twin Vipers but, make sure to slap on some magazine size and reload speed mods.
You do not get anything back and are not allowed to do any other mission until you complete the escape mission. You can still view the starchart and chat with people, attempting to do another mission will force you to complete the Escape mission first.
Best Answer
Not currently, no. As of this writing, the only effect that alignment has is in the cutscenes. It is planned to be used more in the future, but it is not clear for what exactly.