There is some controversy in the medical literature about whether or not stretching is beneficial or possibly even harmful.  One of the theoretical reasons why stretching might hurt include the fact that stretching can produce an analgesic effect, which might allow more damage to occur to the muscle.  In addition, most muscle damage during exercise occurs during the normal range of motion of the limb, making stretching, at best extraneous.  However, consider that the vigorous stop and starts of Fartlek training may induce damage to the muscles, as opposed to "overstretching." 

Perhaps trying a more continuous training approach which might help decrease the pain. Talk to your doctor and trainer about this option.