Absolutes (like "always") are often not as absolute as people claim. The NPCs are there, originally and ultimately, to provide actions that enhance the story. So, "How will this be a better story?" is a legitimate question to ask. Reasonable motivations often end in boring stories, and we may need to apply unreasonable motivations to make them interesting.
In which case we have just bad and lazy writing which defeats any interest your plot point might have added. Yes it is reasonable to ask, "How will this be a better story?" But too often writers in any medium, whether movies, novels, video games, or an RPG, have an idea where they want to go but no clear picture of how to get there. The result is NPCs (or protagonists!) jumping through hoops of stupid or arbitrary because "plot" or "reasons", and not for any clear purpose. You may get away with it occasionally, but generally these moments jar the audiences suspension of disbelief, emersion, and sympathy for the characters.
For example, often action adventure movies require that the hero overcome the villain. To do this, they often require that the villain be utterly stupid in a number of (now trite, predictable) ways, so that they throw away their advantage doing something stupid and allow the hero to win. This reduces the stature of the hero, and render a dramatic situation slapstick comedy subject to being mocked. An extreme case of this is probably 'Cobra Commander' from the '80's GI Joe, who is almost entirely guaranteed to undermine any chance of victory he may have in every single episode for reasons that are often inexplicable - even a moron would have a hard time being so stupid consistently. A similar situation occurs with Azmodan in Act III of Diablo III.
Alternately, and this is increasingly common in summer blockbusters, the writer may have this idea for a spectacular special effects set piece, but no clear idea why it should occur. Well, logic be darned, the needs of the CGI spectacle must come first! The results can be entertaining scenes in bad stories. Without a hundred million dollar budget for visual spectacle, I'd focus on the story.
I hold that you want to reduce the freezer logic in your story as much as possible. The more obviously things in your story happen purely to serve the story, the more contrived your events are, the more unlikely your events are, the less reasonable the motivations of the characters seem to be, then the less well you've done your story. The goal of the writer in most cases is to recede from the foreground, so that his hand on events is not repeatedly being observed. The characters themselves must live.
In this case, "How can I make a better story?", is answered by, "Make your NPCs have interesting motives."
And if it is a case of, "The story is paramount.", there really aren't a lot of ways to make the case of the BGO has it personally in for the PC interesting and satisfying to the audience. In order of the PC's sacrifice to be meaningful we have to establish before this scene that if the BGO helps the BBEG, they are unbeatable and this really is 'the only way'. If there is any other circumstance, then this diminishes the NPC or the PC, and that in turn diminishes the other. If the PC turns the tables on the BGO and wins, the BGO now looks foolish. If the BGO turns the tables on the PC, and double crosses the party, the PC looks foolish. Either diminishes the story.
There are probably more interesting ways to go with the opposite - the BGO actually cares for the PC and thinks the BBEG is invincible and is trying to protect the PC or subvert them to form a third front. Some variation of "Luke, I am your father." or "Darling, I have always loved you." Of course, that requires a bit more set up that a spur of the moment act like this probably has had. Or course, "I've always hated you", equally requires a personal relationship exist between the PC and the NPC before that works as well. The previously undisclosed personal vendetta of mook #5 in scene #17 isn't that interesting.
I think in general, if a PC makes a sacrifice, then the unprotected BBEG is expected. The big question becomes, "Why?" The BGO needs some legitimate reason for throwing away a chance at victory, and some reason to believe that after the BBEG goes down they be able to escape the rest of the parties vengeance.
