People are inherently good and evil. By our choices and free will we may determine how good or how evil we are; thus, good and evil are integral parts of humanity. Humankind cannot be perfected or it will cease to be what it was. Personally, I like the approach used since the eradication of the DO would have been far too simple a plot line and rather predictable. Instead the book made an observation about the nature of humanity and the nature of good and evil. Each term requires the other to define itself - if there was no evil then what meaning would good have? Without one or the other everything would just be and that is certainly no state for humankind to exist in. I mean look at how many character you grow to love in this series at some point make a wrong choice, act out of rage, are envious, are self-centered...they are all flawed, but yet they are lovable characters. As such, I don't think the DO would be impossible to destroy in the series (though I find the suggestion of Padin Fain replacing the DO intriguing) I merely think that doing so would destroy all of creation just as much the destruction of all good.
Concerning the seals, it seemed to me the idea made sense since the DO was nearly free from the prison and so to remove the seals (seemingly the last thing in its way) would have fully unleashed the DO on the world. Rand encountered the DO and faced him fully; however, the DO was contained to a location versus being free in the whole world. Rand is a human and thus also contained to a location. The only way then to have these two opposing forces directly clash was while the DO was contained and once Rand had control of the DO it was safe to remove the failing prison and build it anew (no more patching). What I don't understand is why the followers of the DO didn't just bust the seals when they got them since that should have ended it all right there since Rand would never have been able to get the "genie back in the bottle".
About Fain, I was thinking that his power might somehow had been required to reforge a new and stronger prison for the DO. Clearly RJ or BS didn't follow this line of thought but given the nature of Fain's power it seemed to be something wholly distinct from saidin, saidar, and the true power. Furthermore, what is the counter force to the true power since everything is about balance - it seems unequal to pit it against a split force...why not some power of creation? I felt like their might have been some allusion to this idea when Rand discussed his weaves against the DO being pure and not using the sub-powers such a fire/air/etc...but some direct resolution on that would have been nice.