My oldest is allergic to milk, eggs, peanuts, tree nuts, and mustard. In the past, he has sat at the allergy table. It's peanut and tree nut free, but does have his other allergens. What we did the last few years is to have a buffer where no one with "spillable milk" sat in the seat on either side of him. We also had a spare lunch in the nurse's cabinet (unopened box of crackers, a couple of Sunbutter squeezes, and a safe granola bar). It wasn't gourmet, but it could get him through the day if his lunch did get spilled on somehow. His first year in our district was in second grade and it took a few days to get things rolling with friends at the allergy table, but his teacher helped, as did the guidance counselor. Last year, his table was very popular because kids from more than one class could sit there.
This year he has the option of sitting at the allergy table or at the head of his class table (with cleaning precautions in place). It's a big step, but he's excited and feels ready.