I forget where it's said, and I don't have time to find it at the moment, but I'm pretty sure at some point it's said that there was only allowed to be one child from each descendant. No one knew that Alvis had Lopt blood in him (I personally don't think think he knew it himself), as he was a bastard child. The Lopt Clan discovered that there were two descendants and orchestrated events to bring them together. Alvis only went along with it because he got the throne. In the 2nd generation, when he finally realizes what's going on, he defects and releases the children he's supposed to kill. IMO, Alvis thought the deal was overthrow the government to get the throne and a wife.
TL;DR Alvis got screwed over just as much as everyone else.