Primordial Warlock

Doesn't seem inherently villainous to me.  You could easily use it to make a character like Elsa, from the Frozen franchise.  Last I checked, she's not a villain.

So far only 2 of villainous subclasses seem villainous. Hell Knight fighter and Pestilence cleric. The rest aren’t inherently villainous.

Very few options could be inherently villainous. Just like how very few are inherently heroic (there’s devotion paladin I guess, but much beyond that any of them can be a bad guy). It’s never about the tools, it’s about how you use them. It will come down to role play choices.
These subclasses do, however, seem to give an easier path to be a villain, or at least an anti-hero.

I don't think the word villainous means what wotc seems to think it means.  In fact, I can't figure out what they may think it means.

Path of the lich kind of is, as its powered by devouring souls. But yeah most of these really aren't. Hell Knight/pestilence druid and path of lich.  This one, the patron is sure, but there is no real requirement that the warlock align with the patrons ideology. Now if you don't I expect the whole planar ally feature to go south for you. But just don't use the level 14 crap feature.