There were no directives or the contradicted the actual goal. Well maybe they don't but the player can't do both the stated directive and achieve the overall goal. As for disarming while they are talking that's not a good plan. Firing before being told is usually very bad.
One other thing about the early missions. Since you seem to be trying to follow a canon time line doesn't having even one Vorlon die contradict the show? I can't remember where but isn't there a reference to a Vorlon death (possibly Kosh) being the first one in ages. I took that to mean none had died since the Shadows went into the 1000 year sleep.
On the other hand there is nothing to say the Vorlon fighters are actually flown by Vorlons. They could just be telepathically controlled.
That's actually true, Kosh was the first Vorlon in ages that died.
There are references that unlike the Shadows, which mostly use members of lesser species, Vorlons Remote control their Fighters.
Although not mentioned, telepathy is most likely the way. Not mentioned in the show, thus not canon.
On the other hand, it is mentioned in the show ( at least two times ), that the Vorlon ships are sentient beings
( season two - where the crew of B5 uses Kosh's ship to hide President Santiago Doctor from EA ), the Doc said that the ship sing to him
Also after the death of Kosh Naranek, his ship cremated itself in the sun.
In season 4, Kosh Ulkesh's ship leaves B5 on it's own while Kosh Ulkesh and ( what's left of ) Kosh Naranek are fighting. This could be canon
We can also assume that the Vorlon fighters are sentient beings, capable of fighting on their own.
And as long no Transports, Dreadnought's ( which are always manned ) are destroyed, it doesn't matter how many fighters get destroyed, at least before the fight with the Shadows begins and Kosh dies.
Remember, Kosh died AFTER the Vorlons engaged the Shadows, while the Transports and the Dreadnought has been damaged, none of 'em where destroyed.
The fighters otoh...