I recently read where someone had a trunk leak that turned out to be from the rear window where the defroster connection is. Regardless, if you've isolated the source to what you found, then I'd RTV it since you're not under warranty. As far as rust, pull the liner and carpet out and let everything dry well in the sun. If you have any surface rust, clean it up and prep it, then button everything back up. It's a trunk and as long as you stopped the leak, you should be good.
07 GT Prem: Alloy, MT, 3.55's, Steeda CAI w/Brenspeed tunes, FRPP Stingers, 275/40/18 Goodyear Eagle F1 A/S on SVT Cobras (OE GT500's), 14" shorty, Wheelskin side scoops & qtr window louvers, A-H rear window louvers, SHR honeycomb blackout panel, Sequentials, Hella Optilux Extreme XY fogs, Silverstars
06 V6: Legend Lime, Pony Package, 14" shorty, Sequentials, Hella Optilux Extreme XY fogs, Silverstars