Hey! - Goblins are not monsters. And I'm not only saying that because I'm an idiot with 50.000 of them in my garden! 
Check out this post: http://ruinsofempire.twilightpeaks.net/forums/index.php?topic=120.0
Now if your character IC believes they are nothing but little monsters, sure go ahead. 
Many Anuireans readily place goblins in the category 'irredeemable monsters', which explains a lot of heinous acts against goblins over the years. Acts that the actor feels are both just and good, perhaps even temple approved (slay al the goblins - spare no one).
The fact though is that murdering goblins is no good act. Slaughtering goblin women and children definitely evil. Good and evil are not relative, and even when justified evil act are...evil.
Now, the murder of goblins might serve some greater purpose and actually save human lives later on (goblins definitely are not do-gooders), but the actual murder of them is not good (at best) and most likely quite evil.
Oh I'm fairly sure that wholesale genocide of pretty much
anything comes under the 'if you are really lucky you might get it counted as
evil but necessary category - but probably not'. Forced relocations (ethnic cleansing in modern parlance) with bloodshed restricted to combatants as far as possible (an elastic term) and in response to ongoing raids and other provocations however? Surely the evil thing is to sit by and do nothing while the goblins raid freely?
So by all means Elenie can argue that the goblins can live as long as they behave themselves, the Aegis will simply wait for the goblins to (inevitably in their view) betray the Elenien trust and then act (downside of being lawful good and serving Haelyn, if a noble really want to do something you think is stupid you let him), but from reading the post Neils linked if someone is going to try and argue that goblins are not a race wedded to evil that worships demons they are going to struggle
As for the Countess, she should remember that pride cuts both ways - only a foolishly proud person picks a fight with major dignitaries over a minor point of protocol - the captain should, in my view have been less '
do as I say scum' and more '
with respects your worships, I am but a humble soldier sworn to loyalty given orders - pray accept my duty to follow them as best I can. My orders, give to me by my lawful commander, are merely to escort the prisoners to the castle to ensure they pose no threat to the city and ask of your honoured selves that you discuss their disposal on sundry other matters with the countess. Since your honour demands they stay in your care milord, might I request that you lead us to the castle and oversee the guard - no doubt the honoured pontiff will swiftly satisfy the countesses concerns over the safety of her citizens, etc, etc' - the same actual command, but far more likely to succeed and avoid causing offence.
From a purely pragmatic point the countess sending out her men with orders to kick the party around and treat them like peasants was dim - yes she can slaughter the PCs - but what does she expect to occur in the coming months? She is a person of pride and power - but so are they. The key point to remember in such case is that you
never argue in front of the minions and you
never contradict each other - face can thus be saved and honour salved on both sides without severe misfortune.
As it is tired, wounded, party members treated with contempt and disrespect by someone their utter social inferior (a mere captain orders the Pontiff, dreaded Swordmage, various other dignitaries about like criminals? Mook, thy name be Captain Deathwish) who were, unsurprisingly, offended by the countesses' treatment - she could easily have 'ignored' the offence publicly and contacted the PCs afterwards explaining the offence given, the way her authority was undermined, the harm caused by their lack of consideration etc etc - and wound up with
them owing
her, instead of making them enemies.
One wonders if the countess will consider bullying the party at blade point will be rewarded when the wraiths rise to the slaughter in the months to come. I expect she will (honest guv'nor) be
shocked and
appalled at her captains acts (subtext, I proved I have teeth, don't try my patience again) and
grateful in the
extreme (subtext, oh my god what did I do, have a token to see that I recognise the hole I dug myself into) for your aid, may we meet under better circumstances in the months to come (subtext, you turn up and scare the crap out of everyone, we almost had city wide riots with people terrified that wraiths would pour from the sewers any moment, next time call me and we can keep it quiet!), etc, etc.
not of course that the nobility is ever likely to be rational when it comes to pride - indeed they often start from the premise 'I am my pride and should it be offended then I am nothing if I do not defend it' - but they are also prone to being very practical...
