Spoiler alert Why would anyone expect Eugene to...
Be loyal to Rick & company and escape from Negan with Sasha and Rosita? In Alexandria, they disrespected him, treated him more or less like crap, constantly made fun of him and gave him tedious jobs like guarding the gate, which ignored and wasted his prodigious intellect.
Negan immediately recognized Eugene's intellectual value and took him into his cadre of leaders, gave him power and interesting, valuable jobs, and tons of perks: nice apartment, free food, video games, and visits from Negan's pretty wives. Eventually, Negan would probably decide that Eugene would rate a wife of his own. Plus, and probably most importantly, Eugene obtained a Grumbly Gunk.
Why would Eugene even consider going back to Alexandria?
Please no spoilers after Season 7 episode 15! My son and I have only gotten that far in the series.