I dont know how can defense of an insect attack or other cain of attack. The differents plants has differents insects or mushroons or even animal whichone could attack tge differents plants. I think that a extend hermetic cabin with natural gases could solve this problem and environment problem.
For the most part I agree that a shelter would be better. As for the pest control I think cayenne pepper water spray and something else (soap?) combines to keep most everything away and does not hurt your plants. Look up natural organic herbicides.
https://www.google.co.kr/?gfe_rd=cr&ei=j_K_V8W0MePN8geNmaGQBQ#q=organic+herbicide+recipe+list
Apart from Soap Spray and cayenne pepper water spray, Many Professional Exterminators like pest exterminator in Sacramento suggest to Use Indian Neem Oil and plant mint seeds near garden area to get rid of pests.
Let’s start documenting this kind of information on the wiki! http://wiki.farmbot.org/farming/home