Yes, you are correct. As explained in the books, it was the nature of the weave that enabled the Dark One to taint it - if the Dark One really wanted to destroy reality, it could have tasked Lanfear, Moridin, Messana and Aginor with investigating the Bore more closely and they surely would have come up with the idea before Lews Therin did, because they seemed to realize the danger and how the weave was used before the Strike.

All we can really say is the the Dark One's initial motives may have been to destroy or pervert reality without tainting saidin or saidar.

I suggest you be generous and chalk it up to the Dark One not being a terribly original creation, and RJ's general treatment of villains not being terribly committed to their goals nor that bright. For the purposes of the story, all we needed to be told was that the price for using saidin to Seal the Bore was a punishing blow delivered against saidin.

I prefer thinking of it this way, because I think you'd end up reaching overmuch to assign some reason as to why it couldn't work, and without RJ able to make up an answer on the fly or give a more detailed response to a fan question, I think we will never know why.