If he was one with his machines, he could've easily stopped all the traps that the Nerevarine had to go through to get to his chaimber
Surely, he wouldn't be happy with the one mortal that removed any chance he had of retrieving his godhood again? Also, Sotha Sil was crazy. We know this. How do we know just what kind of crazy he was? Perhaps he was the eccentric loner we're led to believe? Perhaps he enjoyed murder, and felt like doing so to the Nerevarine? Who knows?
Besides, it's pretty clear that his specialty wasn't magic but technology- and there's no real way to capture/transfer a soul via technology.
Uhm. Sotha Sil was a mage. It's stated various times. Restoration magic also causes insanity, as shown by Therana, which further emphasizes my previous point.
And it's been heavily implied, if not confirmed by Azura herself that Sotha Sil was dead, as part of her final speech.
"He shed his mortality long ago"...
Seems to me that it isn't as straightforward as it seems.