In networking gear how it's done is using different wavelengths - be it bidirectional, or BIDI as it's called in the trade, using two wavelengths from the 1310~1550nm range (on one side it'll have, for example, a 1310nm transmitter, a 1490nm receiver and vice-versa on the other side) optically coupled together. Or CWDM/WDWM technology that uses tens of different wavelengths on a single fibre and (de)multiplexed together in an external optics units - in all those cases the active parts themselves have their unique WL. If your product is low-volume the cheapest option would be to buy CWDM SFP modules and rip the optics and transducers out.
Mind you that technology is intended for single-mode fibre (9/125um), but for very short distances any ol' plastic straw will do.