There's a few things you can do. By design, it wants to over-write and keep everything up to date, because running an out of date mod is potentially against what the modder wants.
However, for people who love tweaking, it's a bit of a challenge. Here's a few things you can do, and you may choose what works best for you.
[ Simple and Easy ]
1) Make your changes under TempMods. Then, uncheck the Refresh Mods automatically, and play as normal.
2) Make your changes as you normally would, and run the 7daystodie.exe manually, skipping the Mod Launcher completely.
[ Advanced ]
3) Make your changes in the files, then host the files somewhere, and create a My mod to download the full mod, then download your changes.