The Council of Europe convention on human rights has an article forbidding the enforced disappearance of persons, containing substantially the same language as the Rome Statute. The notion that the European Court of Human Rights, operating under the auspices of the Council of Europe, could find no statute under which to bring action against Sweden that dealt specifically with enforced disappearances, and therefore had to bring action under a torture cause, seems to be contradicted by evidence.
ETA: But as you say, that's not really the problem. Vixen names ECHR as the court that allegedly found against Sweden for the disappearance of the two Egyptian deportees. But the Rome Statute she says Sweden was found to have violated is enforceable only in the ICC -- which although not technically part of the United Nations was at least founded under its authority. Not only is Vixen wrong, she cannot be correct. Separately there is the claim that the court which did find against Sweden was forced to do so for an unrelated crime because the relevant human-rights statute, enforceable by that court, had no provision against enforced disappearance. I find that unlikely given the prevalence in various forms of international law of a statute to that effect, similarly worded. It's more parsimonious to suppose that the court considered a properly-brought cause of action that did, in fact, correspond to the actions Sweden and Egypt are documented to have undertaken.