The fact that N's Zekrom/Reshiram (Dragon tries to refuse being spliced with Ghetsis's Kyurem, yet when you--the always morally-upright protagonist--tries to fuse the dragons, neither dragon objects... I think this indicates that Zek/Reshi struggled because it wanted to stay loyal to the trainer it chose and not be used for evil. Not because it minded being reunited. Because the three dragons were originally all parts of a same being and it was conflict that tore it apart, I think being (partially) reunited doesn't bother it. Now that Zek/Reshi and Kyurem are on the side of the same trainer, they no longer have a reason to be in conflict.
Of course, this is all based on the assumption that Gamefreak created an unquestionable, morally-upright protagonist. ;)
On the topic of morality, what is it that makes it okay for the protagonist to keep a godlike pokemon in captivity? Using them for sport may not be evil compared to using them for world domination, but given that the entire process of summoning these legendaries is questionable, it feels like legendaries are treated like spoils of war. Is there an answer besides the protagonist always being right?