Not really. In a more precise language, what you are describing is that temperature is an ensemble property of particles, and individual particles can store more energy (in case of a gas: mostly be faster) or less than the average. However, this applies to cells, heat sensors or anything else that would “feel” the heat too. Those are still sufficiently big that they are primarily affected by temperature as an ensemble property of their molecules.
For example, a single fast air molecule hitting a cell usually will slightly heat it up as the impact dissipates over the many molecules of the cell. Heating up the entire cell to the extent that it suffers heat damage would take so many fast molecules to hit it in a short time that such an event is extremely unlikely. The same applies to a single ultra-fast molecule holding all the energy. This is rather something you might get from radioactivity and similar.
Now, a fast air molecule that hits a protein (or similar) might disintegrate it, but that’s not a critical damage to the cell as this happens all the time and proteins get replenished by the cell. (This is also why the critical molecules such as DNA need to have a considerable heat tolerance to keep the incidence of cancer at a tolerable level.)
Consider this an experiment, there is a room built to constantly supplies some extremely hot air from one vent and some extremely cold air from another vent (not directly blowing onto the person). Walking into this room you feel warm as the hot and cold air average out to warm temperature.
The coldest temperature at which you have air is roughly −190 °C. If we assume that the heat capacity of air does not change much with temperature, that your warm temperature is 30 °C, and you supply hot and cold air in equal rates, your hot air would have to be 250 °C. That’s a temperature that humans can withstand for a short time (just put your hand into a heated oven).
Thus, we do not even need to think about whether the velocity distribution of particles equilibrates to the Maxwell–Boltzmann distribution faster than it reaches your skin.