About the soldiers:
All characters are assigned to various AI groups - think of these like teams. Fights can be arranged by setting one AI group against another. So the first thing I tried was to force the AI group for the soldiers to be non-hostile to your group. No effect - when I left the tailor's shop, soldiers still attacked. Oddly, not all attacked - and the ones which didn't attack also didn't talk, and were even easier to kill than the attackers because these ones didn't even fight back when I hit them.
So the AI groups were obviously messed up. Next trick: force all soldiers in Kralendijk into the normal AI group for Dutch soldiers. That worked - I could then leave the shop and not be attacked.
Then I finally wrote some code to first make every soldier in Kralendijk report what AI group he was in, then set him to the AI group for Dutch soldiers, and then put him into "Guardian" mode, which is the normal mode for soldiers - it makes them stand still unless one of them is attacked, and they can talk to you. For good measure, since you reported that Antigua was also giving trouble, I did the same for the Antigua soldiers (except that they went into the AI group for British soldiers, of course).
Some of the soldiers in both Kralendijk and Antigua reported being in a group set by the opium quest, while others were in a group for corpses! Evidently the opium quest is failing to tidy up after itself when it sets the ambushes for you when you're carrying the stuff.
Meanwhile, here's a savegame with the Kralendijk and Antigua soldiers all set to their proper AI group and back in "guardian" mode, and with you standing outside the tailor's shop not being attacked. You should now be able to continue the "Kapitein of Kralendijk" and "Elizabeth Shaw's Disappearance" sidequests. I'd advise not trying to continue the opium smuggling quest, and I'll disable that quest entirely in the next update.