We have no choice but to apply these theories. The alternative would be to do nothing until they are perfected. That would be negligence.
Antidepressants do not have a 100% success rate. Nothing in medicine has. That doesn't mean they shouldn't be used.
> In physics this would be blasphemous.
Not really. Plenty of theories ended up being revised when humanity's understanding of the world improved. They still had real world applications: even though they were imperfect, they were good enough for a wide variety of uses.
We don't fully understand depression. We don't even fully understand how some medications work. However, we have studies showing that by taking these medications patients improve and mortality decreases. That's enough to justify their use.