The careful issue here that many of us feel uncomfortable admitting is that being alive necessitates death. This is one part of life: Life is suffering (many Buddhists eat animals) Even the tofu and the rice requires killing not only plants, but animals too - those harvesting machines don't pause to let snakes and rodents get clear before they cut, even if it did there would be the insects to consider and all the displaced species tat would otherwise live in the place of those fields.
I feel there is a partial solution for this moral dilemma, which is to know the life before it is taken. Meet the sheep and the cows, walk in the fields and get out on the water. Get to know the farmer and the fisherman who bring that food to your table and help them by supporting their business. Get to know their practices and lend a hand. In all likelihood when you meet that local farmer, fisherman, hunter or gatherer you will come to enjoy your food more and you will certainly have a better sense of what it takes to keep you alive.
For more information about locally grown food check Out Meet Your Local Farmer from Mother Earth News and Sustainable Table. For information and resources about seafood check out Sustainable Fisheries from MarineBio, Sustainable Fisheries from WWF and Sustainable Seafood from Earth Easy. To meet a local fisherman or Farmer go for a walk, ask around and encourage your neighbors to do the same.

Cory's Dr Green Blog Posts:
Small is Beautiful
Give Organic a Chance
Beekeeping
No Work Farming
Growing Organic