Wild deer are hosts to wasting disease (mad cow for deer), a deer strain of TB, and brucellosis. I'm not positive, but the way some diseases spread, I'm thinking of the TB specifically, is by feeding nose to nose. If there aren't mobs of them grazing the same spot, that's probably a good thing. If you have any doubts, I would suggest looking into composting, using Black Soldier Fly Larvae, vermiculture, and chickens. I'm fairly certain that the more different groups of animals through which you cycle the stuff, the less likely disease will be able to pass from the deer on to you. Also, if you collect and actively compost the deer poo, you will be making strides into eliminating manure-borne disease and parasites in your area.
Unless there are problems with disease in your area, though, I don't think extreme measures are necessary, though I would be interested if a nice, old-fashioned, high-temperature compost would kill anything the deer left in their scat. Much easier to manage unless you're cultivating BSFL and worms anyways.
I'd be interested if there were anything besides the stuff in the garden that you could sow as groundcover that they would eat preferentially to your food crops, fertilizing as they go, or something you could sow on the edges of the runs they use, just enough to draw them, and just sparse enough that they need to keep moving.
Though I think in some areas where they are considered a nuisance, it may be illegal to feed deer.
A human being should be able to change a diaper, plan an invasion, butcher a hog, conn a ship, design a building, write a sonnet, balance accounts, build a wall, set a bone, comfort the dying, take orders, give orders, cooperate, act alone, solve equations, analyze a new problem, pitch manure, program a computer, cook a tasty meal, fight efficiently, die gallantly. Specialization is for insects.
-Robert A. Heinlein