Simple. Stryker's an evil, lying, scheming son-of-a-gun. It would be easy for him to blame a mutant for Munsen's death - the fatal stab wound could be blamed on a Wolverine claw or a Weapon XI blade, for instance.
Easy. John Wraith explains Fred Dukes' weight gain by saying 'we all have our own coding mechanisms' - in other words mutations can progress, appearances can alter. Creed flees the island, becomes increasingly feral, lives out in the forests, eventually in wilds of Baffin Island, turns into some savage forest creature, perhaps even contributing to legends of the Bigfoot.
He may have been alerted to Cyclops by the power display at the school, just as the attack on the White House alerted him to Nightcrawler. He could easily have traced Scott to the island. There's nothing to say all those mutants had been there for six years, so don't try claiming that one. Discovering that Stryker was linked to the government and that he was collecting mutants for experiments would mean it would be unwise for Xavier to go to the authorities, especially as he had no evidence outside of telepathy and his secret Cerebro machine, and he's not a physical fighter type who would storm the facility, so he bided his time and waited for the right moment.
See, it's easy if you have a brain!