First of all, you are confusing temperature with heat. These are two different things. Temperature is the average energy contain by the individual particles in a given region. Heat is the total energy contained in the region. To illustrate the difference let us consider two different situations. First consider an oven that is heated to 100 degrees Celsius (212 degrees Fahrenheit). You can safely stick your hand into such an oven and leave it there for several seconds with out doing any damage. However, if you stick your hand into a pot of water that is at the same temperature (i.e. boiling water) you will immediately scald your hand. Why the difference? The difference is that the water is much, much denser than air. You have a whole heck of a lot more molecules per unit of volume in the pot of water than you do in the air in the oven. So, while the individual particles all have about the same amount of energy (thus the same temperature), there are a whole lot more total particles in the pot of water and, therefore, a whole lot more heat. So, what does this have to do with the question? Well, the thermosphere is the outermost layer of the atmosphere. For all practical purposes, it doesn't really have an outermost boundary. It just gets thinner and thinner until it merges with interplanetary space. The air layer is so thin that it actually contains very little heat despite the fact that it's temperature can exceed 1,800 deg F. (I don't know where you got the 3,000 deg figure from. My number comes from the Earth sciences textbook from which I teach that course.) The real danger to the dust as it comes into the atmosphere is not from the ambient heat of the upper atmosphere. Rather, it comes from the frictional heating that occurs as these very fast moving object enter the atmosphere. Unfortunately, this aspect of the questions gets somewhat beyond my area of knowledge. So, I will have to let someone else carry the explanation on from here.