Since TLE Elements are in essence mean elements, is it possible to generate a TLE from instantaneous Kepler elements?
It's possible, but not preferred. As you point out, TLEs are mean elements using the SGP4 theory. The recommended approach is to propagate an ephemeris from your instantaneous Keplerian elements using whatever force model configuration was originally used to solve for the Keplerian elements. Then using the ephemeris perform a least squares fit using the SGP4 theory to solve for a TLE that when propagated over the same time span as your ephemeris produces a minimum RMS by treating the cartesian elements of the ephemeris as your measurements.
Be sure to keep your coordinate frames consistent as well. SGP4 and TLES are in the True Equator Mean Equinox of Date (TEME of Date) coordinate frame. If your cartesian elements from your propagated Keplerian elements are not in this frame you'll have to convert them to TEME of Date (or vice versa, convert propagated TLE coordinates from TEME of Date to your frame) before calculating the position residuals.