maybe a bit late but here is how i solved that problem
i set a RP2 sorting machine to automatic cycle to extract the re-enriched cells (no unnecessary lag by timer ticks). they passed an item detector which activated a state cell. this turned the breeder off for a short time (economical use of my uranium cell) and activated a timer to craft new isotope cells. that way i can keep my depleted cells in a stackable form and craft them into non-stackable isotope cells on demand.
if course you can redesign it without on demand management and just spam isotope cells (RP2 tubes are perfect for spamming inputs) but i think the main solution for the original problem would be to use a sorting machine in automatic cycle mode to extract the re-enriched cells.