Not to mention the fact that the PC is highly unlikely to know any of this, anyways. He might know that the majority of beholders and illithid are evil, sure, which is why I don't think it should be a virtue hit to take up the Matron's quest. The PC might intend to scour the underdark until he finds an elder orb that he can prove is evil. It just so happens that when he pokes his head into the beholder lair and finds an elder orb, it won't talk to him, and promptly starts blasting him. I think that absolves him of any wrongdoing, or whatever the phrase is.
Think about what'd happen if he met Solaufein before being turned into a drow. Solaufein might very well try to bargain with him first, but an evil or unthinking PC might attack without hesitation, simply because he's a drow. Or, maybe Solaufein is ordered to kill the PC on a routine patrol. The PC didn't know he was in drow territory, and Solaufein would be inclined not to kill him, but I think he still would. Is the PC evil for fighting a good member of an evil race in self-defense?
That could very well be what would happen with a hypothetical good beholder.
PC agrees to Ardulace's task. Secretly decides to only slay an evil elder orb.
PC, disguised as drow, enters beholder lair to interrogate any elder orbs he finds.
LG beholder sees drow enter his house, and attacks.
PC says "wait!" but realises that against such a powerful foe any hesitation could mean his death, so fights back.
LG beholder bites it.
PC might regret having to slay a LG beholder, but as it is he has no clue that it was LG, and most likely assumes it was evil, then chops off its eyeball.
Virtuous? Maybe not, but the intent was there. Unvirtuous? I don't think so. Misunderstandings are tragic, yeah, but not evil.