Tell it to only update on launch. If you then ONLY launch the game through the Script Extender, this doesn’t count as a steam launch, and it shouldn’t update. You don’t necessarily need to be using any SKSE mods to launch that way, it just bypasses the normal launch process.
At least, that’s the way it has always worked in the past. If you installed SKSE through Steam, YMMV; just get it direct from the dev website.
Edit: Just tried it out, and this mostly works. “Online Services” are disabled until you update, so any Bethesda.net mods installed inside the game itself may break, but mods installed from Nexus appear to be fine.