So what I originally wanted is possible, with a little python scripting.
To achieve this, a fcidump file containing h1 and h2 needs to be created by moplro.
This entails running an SCF in molpro calculation prior, in my case a HF calculation.
From this SCF, the orbitals have to be stored.
Now in pyscf there is the "tools.fcidump.to_scf" function, which can be used to read in the h1 and h2 and parse them correctly. They will however be given in terms of the Hartree Fock orbitals.
The output of the function "tools.fcidump.to_scf" is a "scf" object. Use its method ".run()" and you will rediagonalize the HF hamiltonian. This generates all the data you need in order to run the FCI algorithm of pyscf with respect to the same integrals as molpro. Now from the fcivectors obtained using pySCFs FCI method, density matrices can be generated.
These density matrices are incompatible if read into molpro. This is because molpro expects density matrices to be given with respect to the integrals that would be generated within the basis set indicated in the molpro input (i.e. sto-3g, aug-cc-pvdz or similar).
To resolve this issue transform the density matrix back into the AO basis using the orbitals and hence generate density matrices that will be identical to molpros density matrices.
I wrote a short Pythonscript that does all this, of course you will need molpro input data, as described, the fcidump file, the orbitals and alos pySCF.
At this point it will probably only function for atoms. I tested this so far for Be sto-3g.