you can disable SCT tree reference update, but then you might end with unresearcheable technologies.
as for why SCT requires automation 2, because it unlocks components, that are required for making science pack, at least when you play with angels + bobs.
i was thinking about setting sct tree linking to be off by default, but so far there was only handfull of mods, that actually messed up tree to create cyclic references. still if there will pop more mods, i might remove dependency links ... but then again, it might result in unresearcheable stuff.