There's no way a gravel filter can make your tank more dirty than it already is. You could use it improperly though, when you siphon dirt out of the gravel you have to make sure you dont go too quickly or you will just be stirring things up. vacuum in sections and go slow so that vacuum has time to suck up the particles. If you stick the vacuum into the gravel and stir things up, then move to another spot without waiting a second to catch it all, you will have a problem. But just give it some time, in about an hour or so the particles should settle and the filter will get some of it out, then just resiphon I don't really think theres a need to change the water for dilution.
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Only one answer. Aliens.
A number of things could have caused his death. It could have been the year old gunk that was stirred up by the gravel, or the huge amount of new water that was put in (which you dechlorinated correct?), or the stress of the water changes, or the cycle was thrown off by the new water plus old muck, it could be a number of things but it's probably not a good thing to change the water so much in one day the gunk would have settled in an hour or two.
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