Can two lone pairs in different orbitals make a chiral centre?
Chirality refers only to the positions of the nuclei. So, if we have the situation you described where one Carbon is bonded to two other atoms (e.g. CX$_2$ or CXY) it can never be chiral. (i.e. a three atom molecule can always be superimposed on its mirror image by a single rotation)

Now, why don't we consider the atomic and hybrid orbitals  populations when assigning chirality? This comes down to the fact that the atomic and hybrid orbitals are just a helpful tool for rationalizing/predicting the structure and reactivity, but they are not representations of the actual wavefunction. The true wavefunction is defined by a set of ''molecular orbitals.'' These orbitals always have the same symmetry group as the nuclear coordinates. In this case, there is a reflection through the plane defined by the three atoms (some jargon: this is called the C$_{s}$ symmetry point group). So if the nuclear positions are non-chiral, so is the wavefunction. 

(More on chirality and symmetry: http://symmetry.otterbein.edu/tutorial/applications.html)