Does it not seem like a huge design flaw that a monster's soul is purgatory-bound regardless of the content of that monster's character? Say I were accidentally bitten by a werewolf, then lived my life as a good human afterwards, why would I thus be deserving of purgatory? Or is it actually a problem that God just forgot about where he doomed 30 million souls to another kind of hell without necessarily due cause?
According to the Supernatural wiki (and what I vaguely recall from watching the show), God created Purgatory specifically to contain the Leviathans - a type of creature He created even before Angels. He was concerned that, left free, they would ultimately consume all of Creation. So he trapped them all in Purgatory and took several precautions to prevent their release.
Eve was a Leviathan (or at least part-Leviathan), also known as the Mother of All [Monsters], and responsible for the creation of the Alphas, who in turn were responsible for all the various monsters in the show. At least, all the ones that aren't directly related to either Angels or Demons.
So, in a nut-shell, all monsters (again, other than Angels and Demons) are descendants of the Leviathans. God had already condemned Leviathans to Purgatory, therefore any monster that dies is also condemned to Purgatory for having "Leviathan blood" in their veins.
Does it not seem like a huge design flaw that a monster's soul is purgatory-bound regardless of the content of that monster's character?
It's not a design flaw, it's simply that monsters are an off-shoot of Leviathans - something God created and later regretted having created. Their consignment to Purgatory has nothing to do with rewarding or punishing the individual soul for the life it lived, and everything to do with keeping all Leviathan material in one place.
Say I were accidentally bitten by a werewolf, then lived my life as a good human afterwards, why would I thus be deserving of purgatory?
Again, when it comes to monsters, it's not about what they deserve, it's about what they are. The rules that apply to humans do not apply to monsters. Sadly, if you were a human transformed into a werewolf (or vampire, or whatever) then you are now classified as a monster. Regardless of how you live your life, you will go to Purgatory.
(Although it's worth noting that what few "cures" for various monster states have been found in the show generally require the "victim" to renounce or avoid succumbing to their monster side. I'm thinking in particular of vampires who can be "turned back" as long as they haven't fed yet. So, if you did get turned into a monster, your only real shot at Heaven would be to find a cure to make yourself human again.)
Or is it actually a problem that God just forgot about where he doomed 30 million souls to another kind of hell without necessarily due cause?
He didn't forget about them. He did what had to be done (according to His own logic.) Human souls that end up being converted into monsters are effectively collateral damage.
As an aside, one of the things I always liked about (early) seasons of this show was the idea that EVERYTHING was out to get humans. The universe didn't care what happened to humanity. That's an important element of creating a proper horror atmosphere, I think. So, this idea that God cares more about keeping the Leviathans contained than he does about any human souls that get lost along the way is quite fitting, I think.