Generally speaking, a hot item in its original container that was on the fire can cook, and should not come in contact with cold raw food on Shabbos. This is called a Kli Rishon. Food that has been transferred to a second location cools off from the cold utensil and is no longer capable of cooking a cold object. This is referred to as Kli Sheini. So, one would presume that once the kugel had been placed on a plate it should now be considered a harmless Kli Sheini, and there should be no problem placing raw fruit on it.
However, there is significant discussion in the Poskim if a solid object which does not spread out along the new vessel it is placed in is affected sufficiently by the cool walls to lose its ability to cook. This is called a Davar Gush. The general consensus, based on the Magen Avraham in Orach Chaim 318 is to be Machmir. Therefore, the proper thing to do would be to avoid placing raw melon in direct contact with kugel, presuming the kugel is very hot to the touch, above 45C or 113F.
It retrospect, there are grounds to be lenient and to judge favorably that your wife did nothing wrong. While the accepted Halacha is to be stringent regarding a Davar Gush, it is more of a Chumra than a true risk of cooking. While certainly one should adhere to a Chumra that has been accepted universally for hundreds of years, we cannot say that someone who mistakenly did not transgressed and violated Shabbos. Additionally, melon is not a food that is usually cooked and does not improve when subjected to heat. This gives us additional grounds for leniency, as whatever occurred to the melon cannot be termed a deliberate and constructive act of cooking on Shabbos.
In conclusion, in the future the melon should not come into contact with very hot kugel, but your wife need not feel guilty over what already transpired.