Vegapunk is the LAST person to say that, considering he just built a WMD and made child soldiers with no will of their own.
No, that's why.
Vegapunk is the Post Time Skip version of Tom: the "science isn't evil, it's how you use it! A ship isn't evil, you should be proud of your creations!" mentallity.
I fully expect Vegapunk to have failsafes for his creations to allow the Seraphim a chance at freedom. You could easily argue he's evil, though, so far I dislike Vegapunk way more than I thought I would because he seems so reckless. We'll see if that's the truth, or just a guise.
For all we know, Vegapunk was trying to draw out the traitor, and anticipated all of this to catch York.
We'll see.