Typically you won't see a lot of rust unless it sits for an extended period of time. The heating of the engine will evaporate any collected water easily.
A carb cleaner is 'safe' to use, but I would try to avoid putting rust flakes down into the combustion chamber.
Maybe get some spark plug grease and just reinstall some fresh plugs. That way when you pull those, that grease will trap and collect some of those rust particles. I'm just thinking out loud, maybe someone else will have a better suggestion.
I would imagine carb cleaner would work. That stuff can be pretty versatile, I used it to clean my brakes. As for rust I would imagine some salt or dirt with a combination of moisture got caught in there somehow and sat overtime.