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The way I see it:
A. Team Skull are the anti-heros. They can't legally steal pokemon from Aether, but Ya Boi and Big Sis ain't havin no high-and-mighty techy foreigners comin in, messing with their home and discombobulating their pokemon. So they tell the grunts to "steal the pokemon so we can sell them for cash" when in all actuality the ulterior motive is to deprive Aether of their experiment fodder and save the pokemon. Edgelord McBlondeBoy is an Aether defective, rescued a Type:Null on his way out.
OR
B. Team Skull works for Aether. Guzma is the "leader" that gets paid by Aether for what he thinks is stealing pokemon, but in all actuality it's EdgeBoy that's doing all the work and making sure his friends at Aether get plenty of suitable test subjects. Guzma and the rest of Skull are totally oblivious to the Frankenstein experiments they're fueling and, if Gamefreak is good, they will all be totally disgusted by it and help the MC take down Aether in the end.
Either way, Guzma is a good guy.
