It would indeed be really bad if the company found out... I like to think that Silas and MC made a decent life for themselves on the run though. The universe is a huge place; easy to get lost in. So long as they didn't cause any trouble after getting away, I think they'd be fine. :)
And I'm not sure if this might help set your mind at ease or not, but... Silas didn't really 'go rogue' per se... You remember the blast that took out their first ship, the Spirit? It was strong enough to hurt MC severely and I believe she wonders at one point if it could be the root cause of Silas' malfunction. There is also a subtle moment in Silas' dialogue later on where he mentions that his creator... personalized him. MC ponders whether or not any illegal tinkering might have occurred, but it's only mentioned briefly. Either of these things could have made Silas the way he is; or possibly a combination of BOTH.
It's left ambiguous, and I think it works best without me trying to over-explain the exact hows and whys... but I think it's safe to say that Silas' circumstances are pretty unique. ^^
Thanks for the comment! I've been waiting to talk about this for a while, if you can't tell. Haha...