Shielding and Ground Loops - RF panel jacks for GPS
The RF return will not significantly flow through the case, for two reasons.


First, even at moderate frequencies, RF flows primarily along the skin of a conductor. Because of this, the outer shield of a coaxial cable or connector essentially becomes two separate conductors - one on the inside surface, and one on the outside surface.
Secondly, at higher frequencies the return path for a signal will "stick" closer and closer to the outgoing path. This is very relevant for EMI in PCB design, for instance.


These effects kick in even at tens of MHz. At ~1.6GHz for GPS, they will absolutely dominate. The return current for a signal propagating down the centre conductor will return exclusively down the inner surface. This means that effectively, your RF return path is already isolated.

So I think your noise issue is with the DC bias used to supply the LNA at the active antenna. Armed with that knowledge, there might be other things you can do to resolve the issue - i.e. improve filtering/decoupling of the DC supply at the active antenna end.

Another thought - do you absolutely need a panel mount connector on the outside of the housing, or could you run insulated coax through an IP67 rated gland and then have an SMA connector on a short trailing lead?