Good question.

I figured they no longer had weapons actually, but that was an error on my part. All of them ran in a hurry. Juna and Aust might still have theirs since they weren't incapacitated at any point. Annara could definitely still have hers if her weapons were secured. Forgot I was going to have Lothren mourn his lost arquebus.

So yes, unless you have objections, you can assume the guards disarmed the characters.