Does disabling them in the launcher work and carry over to SKSE?
		
		
	 
Most likely no. Most texture overhaul mods come as loose files (which means the texture files are not compressed to bsa format) and all the files that mod installed will still be used.
Also big texture overhauls shouldn't come with an esp file that can be disabled through the launcher anyways.
My advice :
1) Backup your skyrim folder from wherever it's been installed. Just rename the skyrim folder to skyrimBakup or something.
2) Bakup your save folder in your skyrim folder found in your documents folder.
3) Go to Steam and use verify local content on your Skyrim. Do not uninstall.
4) Once running a fresh install, use console command:
coc whiterun
and test out the game without having to go through the tedious intro.
5) If it still stutters, diable bethesda's high-res patches in your launcher. (It's one of the few texture overhauls that can be disabled through the launcher)
6) If it still stutters when moving your mouse fast, it'd be best to upgrade to a gpu with more vram. If you're not planning to use ENB, you don't need an expensive gpu. My now old gtx570 with 1.28 gb of vram gets 60fps at 1080p but stutters a little bit with texture overhauls.
7) If things are working fine, use Mod Organizer, NOT Nexus Mod Manger, to install the mods and test out which texture pack is making your game stutter. It will most likely be big stuff like skyrim 2k textures, landscape retextures, serious realistic overhaul etc. If using Mod Organizer, you can simply disable mods by unchecking them so it's really easy to install or remove mods without messing up your skyrim installation.
8) Remember to install all the gameplay related mods you've had before if you want to continue with your old save.
9) If this did not solve the problems or your saves don't work anymore and want to go back to how it was before, restores your bakups from step 1 and 2. There's no need to uninstall Skyrim. Just delete the Skyrim folder and rename your SkyrimBakup folder to Skyrim.