That is fully understandable. I hate to break this to you but your food probably already does come into contact with undesirable substances due to run off, soil and water mechanics, etc...
The biggest issue with shingle roofs (besides the granules) is the same issue with all roofs - insects, debris, and bird poop. That is why most rainwater capture systems use something called a first flush or diverter along with a filter to help minimize those containments.
If you are still worried about the granules (the asphalt hardly leeches anything) you can consider going with a metal roof, or even applying a cool roof coating over the shingles.
For more information:
Read "We are building a new home and wish to include a rainwater catchment system. Are architectural shingles safe for watering food plants?" a Q&A answered by Kevin Holdridge.
Also, check Sean Lintow's blog post "Going Off-Grid in the 21st Century - Rain Water Intake."