You have to be very careful how you ask these questions, because:
1) In general relativity the questions about energy greatly depend on what method you are using to measure the energy and where you are measuring it
2) There is no quantum theory of gravity, although I think that your question can be answered using QFT on a static background spacetime
I don't know enough about quarks, but if you consider, e.g. a diatomic molecule like oxygen, then tidal forces can certainly be strong enough to pull apart the molecule. The resulting separated atoms are in a higher energy state due to being separated (i.e. energy can be obtained by recombining them), but the overall energy is conserved because in order for the tidal forces to pull the molecule apart one of the atoms must descend and reduce its gravitational potential.
If the molecule were allowed to re-form then you could release photons from the process as well as increase the KE of the molecule. These photons would have a total energy less than the lost gravitational potential energy, such that the Komar mass of the whole system (black hole, oxygen molecules, photons) would be conserved.