Vegetable and flower gardens need deep, rich soil that provides them with vitamins and minerals for growth, blooming and bearing. Manure can provide these nutrients naturally and is a valuable soil amendment in the garden. Manure may contain peat moss, sawdust, mulch, manure, grass, straw, wood or any other organic compound, and should always make up a certain percentage of the growing foundation.
If the manure is fresh and not composted, then yes it is killing the plants from excess nitrogen burning their roots. There's also a question of pathogens which may be present in uncomposted manure (e.g., E. coli), which brings up a separate question related to food safety. There's a current discussion here at The Helpful Gardener related to the E. coli outbreak in Germany.
If the manure was already composted, the sheer quantity of it may be overwhelming the young plants. Although you don't say how large your garden is, 2 tons = 4,000 lb. Unless we're talking about acres rather than square feet, such a quantity of manure would lead to a nutrient imbalance.
If such a windfall of manure should come your way again, it might be more helpful to the plants to spread it over the soil in the late fall so that winter rains/snow can compost it or finish composting it and drive the nutrients further into the soil, where they'll be available to plant roots in the spring. Right now, everything is right at the surface.
The problem is that too much manure throws the soil’s nutrient balance out of whack. Healthy soil contains just the right nutrients in just the right amounts. Randomly adding fertilizers and amendments can actually create problems.
When there is an inbalance in soil chemisty, it will cause lots of problems. The main problem with too much manure is if it isn't composted well enough and it will 'burn' the plants up.Too much often makes plants grow faster, but only produce leaves instead of fruit/vegetables. Or it kills them outright.