Exactly. Under ideal conditions (and yes, the conditions in INS were not ideal), if Our Heroes primary concern was the Prime Directive (and that's a big if under the circumstances) they would have stood (standed?) down and withdrawn from the planet as soon as they became aware of the relationship between the Son'a and the Baku, for the same reasons they withdrew from Klingon space in "Redemption".
No. Picard's primary concern was the safety of the Ba'ku. He did not put down his uniform because he violated a direct order, he put it down because the Federation ignored its own rules and he could not fight against these rules from within.
Picard learned the truth while being attacked by Son'a and then being imprisoned by Dougherty and Ru'afo. He can hardly stand down and neither can the Enterprise who is attacked by Son'a warships. It is no longer an academic issue, it is a fight for life and death.