Still a little new here, so I'm not sure how to pose this in the "mad" section and so far, I can't find this speculation anywhere on the site. Still, I can't be the only person who's thought this so I'm gonna keep looking, but in the meantime...
Anyhoo... it seems like everyone (in the series) is assuming that the Baron is Gil's BIOLOGICAL father. Thing is, all we know is that Klaus shows up after being gone a while with a kid on his back that he says is his son. We have no idea who his mother is. We have no idea of the circumstances of his birth. We do know that the Baron has gone through great pains to hide Gil's past.
Talvek discovered multiple stories about Gil's lineage (starting with [this comic]). One involved the sausage maker incident (probably false), and one involved Petrus Teufel, leader of the Black Mist Raiders and a powerful spark himself. This second story is presumed planted as well, but my gut tells me there's a grain of truth somewhere in between these two tales.
So, let's go with the latter story being mostly true - let's assume that Klaus had it out with Petrus at some point during his time when he was off the proverbial grid. Klaus wins, presumably killing Petrus and leaving Petrus' son an orphan. Either paternal instinct or scientific curiosity kick in, and Klaus decides to adopt Petrus' son. Considering who's kid it is, it would cause a scandal if word got out, Klaus is harboring the enemy's son, so precautions were taken. The only people who could know the truth are Petrus (who's probably dead or worse), and Klaus.
I think that as far as Gil knows, Klaus is his biological father. I don't see any reason for Klaus to tell him otherwise.
Recent conformation from the authors of of Klaus being Zeetha's father got me thinking about this again.
I admit, I don't see much resemblance between Gil and Zeetha physically except for brown eye color, but that's neither here nor there (For the record, Klaus' eyes are greyish blue). They could be biological brother and sister. Of course, then I went back and looked at some earlier scenes with Gil & Klaus (and Zeetha). Again, not much resemblance among any of them (though maybe it's just me, but the pic of Zeetha followed by the close up of Klaus, they way their eyes and eyebrows are posed makes a nice paralell in light of the recent news).
And then I scrolled down the page on that first link and spotted the Baronin Wulfenbach who DOES bear a striking resemblance to Gil. Question is, what happened to her and did it happen in Skifander or before? It's looking more and more like I'm wrong about Gil being adopted, but there also still a lot of plot to be revealed.