More than likely, several thorough vacuumings (if that's a word!) of the carpet would have been more than sufficient to remove any fecal material which might have found its way into your home. I suppose if you wanted to reassure yourself that the carpet is as clean as it can be, then you'd use a carpet cleaner (with soap and warm water) on them....although I suspect this has already occurred to you.
Personally, I don't think such a step would be necessary but if it provides peace of mind, if you're still obsessing about it (given your condition), then this may be something to consider.
I'm obviously not a human physician, but it would take ingestion of quite a large amount of fecal material to cause gastrointestinal issues unless, perhaps, one was immunocompromised; then it might take less.
However, normal, every-day procedures such as washing your hands and bathing every day are going to be sufficient to prevent contamination from even small amounts of material which may be in your environment....if, indeed, there's any there at all after your thorough cleaning.
These fears may not be rational ones but they are ones which clearly bother you so should be taken seriously. I think it's extremely unlikely that you're at risk and I hope that you're reassured by my saying so.