I believe civilian ships do not require any resources to build, they simply cost wealth. The only real way you can slow that down is by first never offering any shipping contracts, and second make all your colonies have stable population. This means their colony ships will never do anything and the freighters will only be moving around trade goods, you will slow down the amount of wealth they generate and thus slow down the ship building rate also.
I think that this may be the underlying problem. When growing new colonies, the shipping lines get a lot of wealth from shipping colonists and infrastructure - then they build way more ships than they need to support the trade of a normal interplanetary economy.
Come to think of it, I think that might be the reason that my fleet grew so large: the large civilian economy on Earth was producing vast quantities of infrastructure, which was being shipped in bulk to grow a colony on Venus. Having more than 100,000 infrastructure to support a population of tens of millions on a body with colony cost > 20 is a bit of a corner case, to say the least.