The CIWS has already been modified from base Guass Cannon stats. I'm at early tech levels, but here's what I see when I compare the two.
The CIWS has a range of 1000. By gauss cannons have a range of 20,000
The CIWS is a twin guass cannon unit at size at size 9.4, HTK of 3, ROF of 5 seconds, and fires 4 projectiles from the dual gc's at that time.
A twin guass cannon turret of the same 12,000 km/s tracking speed would have a size of 18.84, a HTK of 4 (with no armor added), an ROF of 5 seconds and fires 4 shots.
-- plus I need a size 4 FC to get the same 12,000 km/s tracking speed. That's using the GC-100's that I have researched as a comparision.
I don't have a current GC-50 design to compare to, but that seems to be the equivalent of the CIWS, in that the CIWS is about half the size of my GC-100 turret, but has 50% accuracy at the close range of 1000 km where my fire-controls would be much closer to 100% accuracy at that near-zero range. So, the main modification to the CIWS system over a GC is in the range.
If the CIWS seems out of balance, then other stats on the CIWS could be modified to compensate while keeping with the same combat mechanics. I'm thinking primarily of the number of shots fired per volley. If the CIWS is designed specially to throw a lot of metal up in short range, last-ditch fire against missile, then I could easily see that the GC's would be modified to provide more shots per volley. Maybe as a default the CIWS gets 6 or 8 shots from its Dual GCs (instead of the default 4) since they are specially designed for this sort of short-range, quick-burst firing. This could also be another line of Technology to research. Since this research would apply only to CIWS and not to all GC's, then the player would then have the option to spend the effort to increase the amount of shots the CIWS could throw up.
Generally, there seems to be an issue with a player's idea as to what this system is. In the current game, a CIWS is a kit-type solution that you can mount on commercial vessels to get some point defense there. I think in a lot of people's minds, what they are expecting is the sort of military, last-ditch missile defense like the systems (Phalanx??) that the USN currently uses on its ships. Allowing research in specific CIWS areas like the volume of fire might allow players to create the sort of system they are imagining that the CIWS is.