Heat is not a property of a system. Heat is a process function. Temperature is a property of a system because is a state function. For instance, the state of a simple gas is given by temperature, pressure, and composition $(T,p,N)$.
Temperature is defined as the inverse ratio of variation of entropy $S$ to changes in internal energy $U$
$$T \equiv \left( \frac{\partial S}{\partial U} \right)^{-1}$$
This is the thermodynamic concept of temperature, which is more general than the kinetic concept that you are considering. Regarding your question, part of the energy given as heat is used to break the bonds and when are broken if you continue supplying energy this will increase the kinetic energy of the molecules.
Moreover, kinetic temperature is not the average of the kinetic energies of all the molecules of the object. This average of kinetic energies is the average kinetic energy. The kinetic temperature is defined as $2/3$ the average internal energy per number density.
At the other hand, heat $Q$ is defined for a given process as the internal energy interchanged which is neither work nor due to flow of matter
$$Q \equiv \Delta U - W - U_{matter}$$
Notice that internal energy is a state function and $\Delta U$ denotes the difference between the initial and final energies, but heat is not a state function and this is why we write $Q$ instead of an incorrect $\Delta Q$.
The concept of process function is most easily understood with the example of a lake. A lake has some amount of water, and this can change by evaporation and raining. You can count the amount of water added to the lake by some raining process, but the lake itself does not have any amount of "raining" or evaporation" only some amount of water. Similarly a thermodynamic system has internal energy but has not heat or work.