You would generate a magnetic field at the center of the colony to deflect solar energetic particles and galactic cosmic rays. The colony would produce compost with biowaste and use that for soil. There are various ways to remove perchlorates from soil. One avenue of research is to find an optimal mix of martian soil and compost to allow plants to thrive.

The points you are making are excellent but I believe solvable. Also we do know if plants can fruit in space. We've already grown tomatoes in space and they are fruits of the tomato plant. And that was zero G.