Atomically thin semiconductors can be readily integrated into a wide range of nanophotonic architectures for applications in quantum photonics and novel optoelectronic devices. We report the observation of non-local interactions of free trions, and strong light-matter coupling of localized excitons in pristine hBN/MoS$_2$/hBN heterostructures coupled to single mode (Q $>10^4$) nanocavities. The excellent photonic and excitonic quality of the cavity and hBN encapsulated MoS$_2$ stem from our integrated nanofabrication approach that does not involve etching through the 2D heterostructure, but rather maximizes the local field amplitude within the MoS$_2$ monolayer. We observe a non-monotonic temperature dependence of the cavity-trion interaction strength, consistent with the non-local light-matter interactions in which the free trion diffuse over lengthscales comparable to the cavity mode volume. For an ensemble of localized excitons trapped at defects in the MoS$_2$, we observe strong light-matter coupling with a collective vacuum Rabi energy of $12.9pm0.8$ meV. Our approach can be generalized to other optically active 2D materials, opening the way towards harnessing novel light-matter interaction regimes for applications in quantum photonics.