I don't think the wings would get used very much, at least not for flying. Not only would there seldom be enough room for wings to be used, but flapping around in a spaceship is a great way to break equipment, or at least send your papers flying. Plus, most birds have really strong legs; in zero-g, they should have enough power and poise to jump to wherever they need to go without the help of their wings.
For creatures with arms and wings, I would suggest that they may opt to cut off their wings for space missions, but I really can't say if bird society would properly accomodate for them back on the planet (I think it would, but that might just be because I don't have wings). Even if the wings aren't removed, they should at least be strapped down firmly to the creatures' backs/sides, to avoid any involuntary flapping. This shouldn't too greatly impact the bird people, so I'd say space architecture would be pretty similar to how it is for humans.
Now, if the creatures use their wings as their arms, like bats for instance, strapping them down is not going to be an option. Instead, I'd think architecture would adapt to make use of these wings. Since these creatures will probably have very long wingspans, I'd think elliptical corridors would be favored over circular ones; that way, the creatures will be able to make flapping motions more easily. I still don't think they would actually 'fly', but they could definitely crawl along with their hands, so having enough room to make that natural flapping motion while grabbing at the walls will be helpful. With more room, corridors may become circular again so people can turn around easier, but width along at least one axis should match up with wingspan.
I'd think that birdlike creatures would be much more comfortable with the modern design of spaceships than humans are; after all, they can and do move in all three axes. Therefore, I don't think they would depart too far from the current spaceship designs: just put everything on the walls, make sure people can pivot enough to turn in any direction and pass each other going any direction, and don't put people in situations where they're stuck in empty air with no hand-or-footholds.
As to your concern over broken bones, I don't think there's much that would be done. Just look at how astronauts don't wear helmets; they're not worried about giving themselves concussions, so the bird-people shouldn't worry about breaking their wings off. If anything, training is better than protection; the added weight of knowing how to not hurt yourself is far lighter than a ship full of pillows.