Although we'd need a seriously heavy-duty hab airlock system to remove as much dust as possible from spacesuits, thus minimizing contamination of habitat interior, the airflow of life support systems will likely keep any stubborn dust particulates airborne and breathable by colonists. It may also cause blockage to air filtration systems. And contaminate food, particularly over long durations.
In short, colonists will just have to, literally, suck it up and deal with the health consequences and develop methods to minimize the dusty risks. And, who knows? The technologies that we develop to safeguard life on Mars might generate valuable spinoffs for life on Earth, too.
ANALYSIS: How a Mission to Mars Could Kill You
So, what should we take from the science behind these medical concerns?
Once any future Mars colonists survive solar radiation and high-energy cosmic rays during Earth-Mars transit; make it through a violent entry, descent and landing; face the continuous threat of a high-radiation environment; set up camp and begin the first day of the rest of their lives on the Red Planet, I think they'll just chalk-up the toxicity of Martian regolith as one of the list of inevitable hazards to live with on Mars. Worrying about toxic regolith contamination inside habitats probably won't be high on their list of concerns.