I would suspect the throw out bearing. it has got an 'inner sleeve' and an 'outer sleeve'(cant find a better way describing it so early in the morning). Now, as the bearing works and wears out a little, these tolerences can get a bit loose. So the two sleeves starts rattling against each other. When you let the clutch engage, you put force on it and the tolerences/slack is temporarily taken up, cause the rattling to stop.
I had the same kind of problem, albeit on a Renault Scenic(diesel). I initialy thought it's the throwout bearing too. Long story short, the gearbox completely died. No oil inside! I was wondering how the heck that was possible, as a gearbox doesnt realy USE oil. Turns out that a small seal on the gearbox was just leaking enough oil to drip-drip-away while riding, and it never left a stain on the ground
So obviously when I got to know about it, it was too late.
I however dont think this is your problem, but I would suggest that when you pull the motor to get the things replaced, check the gearbox seals while you have the time and space, just to make sure.