Your ship won't get destroyed. If there is space combat, space combat will work like regular combat. You explode and die, you respawn. When you land on a planet, your ship will be out of reach from enemies, very static like. It will be a hub for fast travel, I would think. It won't be on an enemies radar, because you won't be able to use it on the planet. This isn't to say that perhaps there won't be a specific mission that involves your ship breaking down and you having to go look for parts to fix it. As always: Take what I'm saying as PURE speculation. I have NO information to back this up except my vision and expectations for the game.

Improvise

I suppose the aliens would have some means of transportation or else they wouldn't be such a "threat" to the guardians and our city. So you could always infiltrate and take over their ship. That could also be beneficial to you if you can keep, customize and upgrade the ship.