ohhh, shit. not really what i meatn to come out of that, more like...When Ike found out BK was still alive i'm pretty sure, at least from what he tells zelgius and from what Elincia tells him at end of P2 that it was like someone told you, your uncle(who had some dark secret about how to do something awesomely that no one else could do) who killed your father, whom you thought to be dead, was actually still alive. Obviously under these circumstances you would feel mixed emotions, mad because you wanted that man dead, but sort of happy because you could learn his secret.
Another reason Ike is not as mad about BK in tower is the fact he knows that BK is Zelgius, who is sort of friends with Ike. Imagine if your friend killed your dad, you were still friends with him but it happened 3 years ago. what would you do?