Nate,
You really think that 1 fighter bay + 3 missiles (what we advice) will unbalance it all?
Look at the FW Emissary:
130pts
hits 4
shields 1
speed 20
turns 45
armour 6+/5+
turrets 2
prow railguns str4 @ 45cm - F
port railguns str2 @ 30cm - LF
starboard railguns str2 @ 30cm - RF
prow missiles str3 @ 20-40cm - F
port launch bay - fighters
starboard launch bay - fighter
-------------------
Now your proposal:
Sa'cea
120pts (incl prow deflector)
hits 4
shields 1
speed 20
turns 90
armour 6+/5+
turrets 2
port railguns str3 @ 45cm - LF
starboard railguns str3 @ 45cm - RF
port ion cannon str1 @ 30cm - LF
starboard ion cannon str1 @ 30cm - RF
prow missiles str3 @ 20-40cm - F
--------------
So what do we have:
differences
FW vs Sa'cea
130 vs 120
45 vs 90
4 RG@ 45cm vs 6RG @45cm
8 RG@ 30cm vs 12RG @ 30cm
2 fighters vs o fighters
HAAA!

The FW Emissary was crap. Sa'cea certainly isn't/
So, yes, I believe you if the Sa'cea should not get a fighter bay. A changed Sa'cea should.
My gunnery Sa'cea:
Sa'cea
120pts (incl prow deflector)
hits 4
shields 1
speed 25
turns 90
armour 6+/5+
turrets 2
prow railguns str2 @ 45cm - F
port railguns str2 @ 30cm - LF
starboard railguns str2 @ 30cm - RF
prow missiles str3 @ 20-40cm - F
dorsal launch bay str1 fighters
Variant:
may swap port/starboard railguns for a grav hook.
Done.
Not much difference to your creations but more manageable and cooler.

And I still do think there should be more fixed forward gunnery.