You're right. But there really should have been some kind of third option, it didn't even have to be an obvious one. If Fallout 1 or 2 had this quest they wouldn't have had a pop up tell you after you escape that you can now kill Braun and transfer admin privileges to someone else but if you had enough science and investigated some computer terminal it probably would have let you do it.
The pre-Broken Steel ending is another example of being really stupid for having no third option, why would anyone not send Fawkes into the chamber if he's with you? The ending of Broken Steel too, why blow up the Enclave Base, why not conquer or at least scavenge from it? Ugh.