Here's what I'd do (and am doing).
Find a line of rods with a lifetime warranty. There's a few out there. iRod has a lifetime replacement on most of their rods for example. Get some cheaper rods for moving baits and then find them on sale or on ebay for even cheaper.
Then, for the bottom contact baits, go as high end as you can stomach. 16-20lb fluoro is the same in dirty water as in clear so you don't need to change much other than going from a brown jig to a black jig.
Finally, if you are worried about redoing setups, buy a roll of electrical tape and get a few extra reels. Have a set of reels for dirty water, and a set for clear. Then you don't have to worry about wasting line or anything, just swap reels. Doesn't take any longer to do that and retie than it would take to pull all your dirty water rods out and load the clear water setups.
I went further and got 13 Fishing reels and just bought a bunch of their trick shop spools and color coded them by line. Then I can keep 1 set of rods, another set of spools and just change the line without throwing it away.