How can STDP fit with reciprocal connectivity?
Consider that elimination of such a phenomena is not ideal. It's been proposed that actual neuronal networks exist under the tension of synchronous decoupling. 

http://www.sciencedirect.com/science/article/pii/S0896627308001281

To answer your question though, you probably should consider that reciprocal connections might not be between two individual neurons. Rather, axons in the cortex are clumped into minicolumns, each one having 20+ pyramidals in supragranular layers. It's conjecture, but it's possible that the reciprocal connections are between different pyramidals within minicolumns (or even different pyramidals within columns or whatever other macro-structure you want).