I would think the composting process would have benaficial microbes over colonize and bad ones. I could be wrong.

Most likely if the temperatures of your compost pile get into the 135 to 145 degree F range that should be sufficient to kill those disease pathogens. If the temperatures do not reach those levels then time will also work, although several years would not be necesary.
You may want to consider being careful where that compost is put and what you plant there, the precautionary principle.