I think a slim profile and large ablative shield are two good ideas. that largely solve both of these issues.
Build something like the TransAmerica Pyramid (without the two white flanges) and put the motor(s) where the foundation would be as to make the building fly like a rocket. Put the motors on at one G and you get artificial gravity, a slim profile and damage equally distributed along the bulk of the ship and most collision will happen at extreme glancing angles.
Stop off near a comet and melt large boulders of ice to the hull. If the outer hull is tiered whipple shields there will be plenty strong and will serve as mount points for the ice. Run simple heating element through it and simplify the installation of ice as ablative armor.
Have all of the storage on the ship be on walls, cabinets, netting, shelves, etc... and bolt all the furniture down. Because when you aren't accelerating you will have no gravity.
When you want to stop, turn the ship around (using reaction wheels or attitude jets) and blow your engines at the target at 1 G to slow down for the same amount of time you burned them to accelerate. This will create artificial gravity again in the same direction you were experiencing it before because you changed the direction of thrust the same amount you changed the orientation of the ship.
You have a nuclear explosion clearing crap from in front of your ship as you slow down, not as safe as the ice, but presumably your engine(s) is tough enough to withstand a nuclear blast.
[1]: https://en.wikipedia.org/wiki/Transamerica_Pyramid