The atom has collided with the photon and has been given some KE by being hit, so is moving faster. Heat of an object is just the KE of atoms in the object (well, and the PE of them too as the atoms are mutually attracted/repelled depending on what sort of atoms and the distances between them).

If the atom and photon collide head on and the energy absorbed from the photon is less than the energy required to reverse the atom's velocity then the atom actually has less KE and will be cooler. Atoms can be cooled with lasers this way.