So, I understand that civilians are responsible for a good part of the terrible slowdowns of the game? I did think that their number was rather excessive but, that's kind of bad. They are very useful in limiting your fuel usage/cargo needs, especially for moving large amounts of infrastructure, and that's particularly important with a conventional start.
Also, does gutting your own civilian sector help at all? I mean, even supposing you do keep them down.... won't the alien races create a million civilian ships anyway? Cause if they do then there's not much point in staying without civilian ships when every race near you do use them...
If civilians are one of the main sources of the slowdowns, then perhaps rather than keeping down your own civilian sector a different, general solution is needed, one that also influences the NPRs. Because only limiting yours civilians shipping lines to a set number with a checkbox does nothing for the ships the NPRs build.
I think a variant of what alex_brunius posted would be good. Perhaps a hard-cap on total civilian ships for each race based on number of populated colonies (Not colonies designated for other matters, like automated mining or fuel depots or such.) That, and when the limit is reached, the ships slowly start to get bigger (so you still have an increase in capacity).
Just a quick example, say, 10 ships for each inhabited colony under 1 billion people, + 5 ships every billion people (so your 5 billion earth gives you 30 maximum ships). Divided between cargo, colony and spaceliner in a roughly euqal amount (I don't know, 4 cargo 3 colony 3 spaceliner every 10 ships). This would keep the number down unless you colonize a hundred planets, AND it would also limits the NPRs, thus keeping down the civilian sector a great deal while still letting you use them for coloniziation/transport, especially considering the ships keep getting bigger.
P.S. This approach you can even rationalize/RP, by saying that there's no need for more ships due to trade (and more populated colonies generate more trade)