When I set "enabled" to false in the weed.json file, I still get "weeds" but they are randomly chosen from the other plants that are available. I tested this with just Agricraft and Mystical Agriculture installed and I get tons of random mystical agriculture crops in place of where weeds would grow.

Is there not a way to just disable weeds completely, as there was in the 1.7.10 version of Agricraft?

You have to set the spawn chance in all JSON plant files to zero or disable the files all together.