You should read the dissenting judge's write-up. You cannot retroactively go back in time prior to the law being adjusted to add "abeyance". Musharraf's measures predate this change in the law. Essentially if something is not a crime today, you cannot make a law next year and then punish me for my acts in the previous year.The Supreme Court has already ruled that holding the constitution in "abeyance" is equal to subversion which is punishable under article 6.
The law does not work this way yet here he has been found guilty of something for which there was no law at the time of his emergency.