Killing Stanley Poole :
You are given the 'choice' to kill or not kill the little worm. They could have had a little more imagination involved. Him running in terror from you would have been good (fun of chasing him down - that little creep might be pretty elusive - after all he had lasted this long...). (Would require special scripting to make it halfway believable - sop scrathch that expensive idea -- lets have the MMORPG represent it...)
Deciding not to Kill him would give him the opportunity to try to weasel his way out of the predicament as he had before. Funny also might be after you let him go, that he tells you something to get you to kill Sofia (thus solving his problem). He then would be off to find a new rock to hide under. You should know that Sofia Lamb was going to have him murdered, no matter what she said to you.
Where was he all those intervening years anyway ? (probably out of Sofia's sight as she might have some questions he would rather not answer). It might have been interesting to find his spider-hole (and stash) there in/near Dionysus Park -- as he seems to have got there barely moments after you drained the place (and those Lil Sisters sure came running pretty fast too...) - and the corpses seem to have kept nice and fresh after 10 years underwater, not to mention various other props).
That whole hyped "moral choice" thing is really such a joke though, as we go thru Rapture slaughtering HUNDREDS of Splicers left and right and nobody seems to care that THEY might be just as deserving to live as any of the 'bosses'. But then, options to sneak by all the opponents would run contrary to the game being first and foremost a 'blast-fest'.
More Canon fodder - Pooles Fate :
Assuming the Player did not Kill Stanley Poole and he managed to elude Sofia Lamb (who lied about her not caring anymore), then what became of him? He obviously was a survivor (lasting until BS2) and the MMORPG takes place not too long after that.
This MMORPG would seek to retain many of the characteristics (and characters) from the original games (you can only add so many 'new characters' before players start saying "This Isnt Rapture any More". We can fill in details and show how many of the characters interplayed (the challenge is making it cohesive with the clues we have been previously given).
So how would a still living Stanley Poole interact?
Is he welcome in New Rapture??
He had resources of some kind to survive so long...
What strange adventures did he have during 'the lost years' ??