Choosing between two object detection model checkpoints
Choosing the model with the lowest loss on the validation set would be more appropriate. There are cases where the lowest loss model also exhibits the highest mAP, but that definitely is not the norm. 

Regarding your question, if you are to choose the model based on accuracy-like metrics, consider what would be less harmful in your specific example. For instance, consider the case of cancer classification, predicting that a healthy patient has cancer (False Positive) might result in some frustration but it is not that big of a deal. On the other hand, predicting a cancer patient as of being healthy might cost his life.