On/off switching of current from USB Tx line
Most USB-capable microcontrollers use general purpose I/Os for this function, so you can assign them as inputs and put weaking pulling resistors on them.  Contrary to what was previously stated a pulldown would be preferable to a pullup, as that would put the I/Os at the same potential as the ground which is presumably also exposed.  Having them at a different potential could mean a small leakage path, which would both waste power and potentially promote electrochemical corrosion or contact etching.  Even with wetted contacts at the same potential, you want to make sure they are all the same metal.

You should similarly disable the USB speed detect pullup.

However you face a more serious problem in that it is extremely difficult to get a truly immersion-grade waterproof seal between wires and some random epoxy compound.  If you strip the wires first, you have to get the metal perfectly sealed to the epoxy, and if you run the insulation through, you will probably get water migrating between the wire and its insulation.

Something like a connector under a screw-off cap with a compressed gasket may be preferable.  Or you could use a bootloader with some sort of inductive or even optical serial interface.

But of course you have to solve the problem of getting power in there without moisture leakage, too.