I think one of the important things to consider about artificial gravity, especially in deep space, is the impact of thrust. Since, especially on interstellar, rockets could be expected to be accelerating or decelerating for the entire duration of the flight, simply doing so at 1 g would completely alleviate the need for any form of artificial gravity.
I'm not sure what other negative effects your thinking of, but radiation comes to mind for me. Of course, you can always bury your human cargo behind some form of radiation shielding and can reasonably expect much of the radiation to come from the nearest star.
For an example of the previous two points, in the case of a Project Orion nuclear propulsion model, it would be reasonable to use 1 g acceleration half way to the destination, micro-thrusters to change orientation, and and then 1 g deceleration to destination with the propulsion plate being used to deflect radiation from stars. While far from a comprehensive solution, I hope this address some of your concerns.