I believe that it is certain types of fish oils that are leading over fishing.
For instance if you were to buy salmon oil and the salmon was farmed raised then farmed issues aside you wouldnt be overfishing.
I believe that generic fish oil does lead to overfishing but if you by fish oil from Wild Salmon chances are they arent fishing solely for the oils.
http://www.seafoodwatch.org/cr/SeafoodWatch/web/sfw_factshee...