Well, physically he just got force pushed against a wall. No beating there. He hasn't been killed or maimed and, I did ask your permission to hold him before and you didn't object.
Considering the liberties you see fit to take with my technology, a little light abuse of your NPCs seems a fair trade.
I hardly call encountering a technology completely foreign to you and after having seen it for under a minute immediatly discerning it's form, function, purpose and method of operation and then proceed to destroy it and dictate what happens when the science of such a reaction is clearly not understood by you looking at it, so I guess it's a matter of perspective.
A little touchy, are we? Using lots of words to say the same thing doesn't make it any more significant - I see a ship make a portal and go through. I see another ship go through a portal. This one seems to be holding the portal open because it is the only ship that insists on floating right near the rift. I reason it is the one, because the others all look like plain old warships. As for the science, the Arbiter's R&D was all of one paragraph long and I was unaware of the Doors discussion, so lay off.
I believe the point Ahnk is making is that you shouldn't be able to do this:
You see a portal. I would imagine so.. perhaps not as spectacular as Deep Space Nine but..
You see a ship come through... as well as other ships.
But you wouldn't see that ship "do" anything but move.
Now, if this happened, yes there might be some connection or something fishy but the point is: did you have your characters question it?
Even so, we are not necessarily saying that the ship couldn't be fired upon. I mean it is only 7m and if it's in range, it's in range.
And if you wanted to rp what you think the coincidental "results" would be if the ship blew up, fine. But know that the person who designed the ship could tell you whether you get those details right or not.
Using OOC motivation for IC action is wrong and sometimes a fine line. If your ships fire on the most important ship there, is it because you as a player know the ship is important or because your character's find or figure it out? It can be tricky and must be played with care.
But then again, this is no different than looking at someone's OOC planet-defense manifest that probably hasn't been updated in god knows how long and set up an attack plan based on what they read those defenses to be as they would also be using OOC information for their gain.
But please take care with the motivations for your actions is all.