Those disruptions led to a rapid expansion in import competing industry because they were the equivalent of protective tariffs.
Were they similar to complete autarky? Yes. But equivalent to tariffs, which also impose price redistribution and rate government collection? Hardly. If anything, Taussig argues that Jefferson's wartime embargo for military purposes, with all its faults, did more for American industry than the next 30 years of protectionist crap from the Hamiltonians and Whigs. Considering that Jefferson's embargo is traditionally frowned upon from an economic perspective, that's saying quite a lot about how bad those tariffs were as policy.