With the scandal going on at FIFA at the time, probably the last thing they wanted was the host nation getting a result overturned... But my guess is that they just didn't check these things properly and they didn't know. FIFA really need to be on top of this sort of thing better. The money they have is phenomenal, so surely they could get a team of people to work on checking player eligibility, especially for every player in any big tournament, to ensure it's fair for all.
But that doesn't exonerate at all our own massive stuff-up here.
I appreciate the sentiment, but don't think that's really practical. Like I said, the sheer amount of international matches being played is difficult enough to keep on top of everything. The additional issue is that ascertaining eligibility as under current regulations would entail accessing birth/citizenship/immigration records (and not just of the player in question, but his/her immediate family), and there's all sorts of privacy laws around that that would make it difficult, time consuming, and costly for FIFA to try to police.
I think we should really think about it this way: we all know (or at least should know) stealing is illegal. Now, if I get caught shoplifting, I can't defend myself by saying I didn't know - the reality is, I either knew, and I did it anyway, or I didn't know, but ignorance of the law is no legal defence. Furthermore, it's not the job of the police, or the Courts, to teach me about the law, but to appropriately censure me for breaking it. So if I get caught shoplifting, I have to undergo the appropriate punishment.
The same principle applies here - FIFA regulations are public (anyone with the Internet can access them), and national football associations should be familiar with them when entering teams to compete in FIFA tournaments. If they don't comply, and get caught, it's their fault and they have to receive the appropriate punishment.