Wow, you have the exact opposite problem I do. I actually try to propagate hickory trees (a sister to your pecan, both being Carya genus). I am surprised to hear that the Roundup is only a temporary setback. Depending on where these seedlings are, you could put down landscape fabric and wood chips, or you could spray with a broadleaf herbicide (that won't harm nearby grass). No matter what you're spraying, read the label directions and do not spray on a windy day.