You've assigned the fire controls to defensive fire, but have you also assigned the railguns to the fire controls?
As for the help designing a CLE, here's an example of a Light Cruiser I use for point defense and sensor coverage, created at (mostly) Ion Engine level tech. I'll take two of these along with a fleet for redundancy. I'm not saying this is a perfect example of such a ship and I'm sure it could be improved.
EDIT: Just saw the age on the original post so my example ship is probably no longer relevant to the discussion, but I'll leave it up anyway as a different design perspective.
Widowmaker II-B class Light Cruiser - Sensor 18,000 tons 501 Crew 2,704.9 BP TCS 360 TH 2,160 EM 0
6000 km/s Armour 7-61 Shields 0-0 HTK 103 Sensors 6/6/0/0 DCR 18 PPV 50
Maint Life 3.80 Years MSP 1,786 AFR 139% IFR 1.9% 1YR 194 5YR 2,912 Max Repair 270 MSP
Captain Control Rating 2 BRG AUX
Intended Deployment Time: 18 months Morale Check Required
Valkyrie Ion Drive 540-M (4) Power 2160 Fuel Use 58.20% Signature 540 Explosion 12%
Fuel Capacity 1,680,000 Litres Range 28.9 billion km (55 days at full power)
Zara Industries S4-200 Particle Cannon (2) Range 192,000km TS: 6,000 km/s Power 10-3.5 ROF 15
Lapua 4" Railgun (12x4) Range 20,000km TS: 6,000 km/s Power 3-3 RM 20,000 km ROF 5
Sleipnir Weapon Targeting Array 192k/6kkps (1) Max Range: 192,000 km TS: 6,000 km/s 95 90 84 79 74 69 64 58 53 48
Sleipnir Weapon Targeting Array 48k/6kkps (1) Max Range: 48,000 km TS: 6,000 km/s 79 58 38 17 0 0 0 0 0 0
Rostov-Tarasenko Magnetic Mirror Reactor 16.9-P (1) Total Power Output 17 Exp 10%
Rostov-Tarasenko Magnetic Mirror Reactor 28-P (1) Total Power Output 28.1 Exp 10%
Tarlov Systems Missile Detection Array 1.24m (1) GPS 120 Range 13.8m km MCR 1.2m km Resolution 1
Solveig Gravity Wave Detection Matrix 64m (1) GPS 12000 Range 64.1m km Resolution 100
Caspian Infrared Detection Matrix 19.3m - C (1) Sensitivity 6 Detect Sig Strength 1000: 19.4m km
Persephone Electromagnetic Detection Matrix 19.3m - C (1) Sensitivity 6 Detect Sig Strength 1000: 19.4m km
This design is classed as a Military Vessel for maintenance purposes
This design is classed as a Warship for auto-assignment purposes