From what I understand you agree that the Pick call did not affect the possesion of the disc in this part "Both player A and B did make a play on the disc, not affected by the pick call, player B catched the pass and both players stopped, noticing the stoppage."
Therefore, it seems to me that your team wanted the disc to go back on the ground of positioning of the rest of players. But this could have been easily solved by everybody (except receivers) taking the positions they held when the call was made.
I find this positioning bizarre, and while THE play may not have been affected, CONTINUED PLAY has likely been affected.
In theory, play stops at the time of the call (and presumably players remain at or resume their positions at that time). Now, inadvertently, the thrower (and presumably the marker) and players A and B kept playing, and player B caught the pass somewhere other than where that player was positioned when play stopped. Although invoking 16.3 here might be correct because the play was not affected, we now have players on the field who stopped at different times and in different positions. If we allow player B to stay in that position where the disc was caught, the defenders could easily be out of position relative to who they are covering because they stopped at a different position. For example, a swing pass into the flat (from one side of the field to another), could leave all the receivers on the O team now all completely open because player B caught the pass well on the break side while all the defenders were fronting on the open side near the other sideline. Continued play is completely affected by allowing this pass to stand.
I also find this result contrary to common sense. Play stops or it doesn't? If this truly is the interpretation, no player should ever stop on a call, because the play doesn't really (always) stop. In my example above, as a defender, rather than stopping on the call, I should keep adjusting my position relative to where the pass is thrown and to the receiver I am covering. So then, if the receiver I am covering tells me I will have to go back to where I was at the time of the call, it will become obvious that that is unfair.
Furthermore, this interpretation is contrary to 1.2: "....rather a method for resuming play in a manner which simulates what would most likely have occurred had there been no breach." Had there been no breach, the defenders would not all be out of position for the next pass. Note that my example is entirely fictional though also entirely plausible and, in fact, I could easily present a whole range of examples that are equally plausible.
In other words, the bottom line is that any defender could have perfect justification to disagree that play is unaffected, and therefore the disc must be sent back and all players remain at or resume the position they occupied at the time of the call.