It's doubtful this problem is being caused by a soil borne fungus. In fact, it sounds more like the plants could have gotten too cold. I don't know about the holes in the leaves, but marigolds are very intolerant to cold weather and will quickly turn brown if the temps get too chilly. These are tropical plants that do best in hot, sunny spots. Also, they need to be in well drained soil. If they are sitting in a very wet and very cold spot, they will be miserable and start to wilt and look really bad. In northern gardens, marigolds are best kept in a protected location until mid to late May depending on the weather.