It would be crazy if he is Elena son, because If he is, then he tried to kill or capture his own sister, Shiho( haibara)
I personally think he was trying to save Haibara by having the secret police take her away from the 8th disconnected train cart, but vermouth and Akai ruined the plan in one way or another. However, he might have wanted to take her back to the BO alive as well for a reason I don't know, as he even tried to reveal Akai to the BO just to get deeper and get revenge on Akai for causing Scotch's death.
He didn't even react to much to the fact "Shiho" who was really Kaito was "Killed" in the explosion
I will put it simply, I don't think he is a brother to the Miyano sisters or a child of Elena, he could be a distant relative, or cousin, or not at all related to the Miyano's, I could be wrong
However I am not one bit surprised that he has foreign blood, I expected that since sometime now