8 "Unanswered Questions" From Avengers: Endgame, Explained
7. But Wasn't The Whole Point That Creating Alternate Timelines Would Ruin The Universe? Isn't That What The Ancient One Says?
The Ancient One was referring specifically to the Infinity Stones creating dangerous alternate timelines for her. If her Time Stone is lost to Bruce Banner in a different timeline and never returned, then the future Sorceror Supremes have lost their life purpose.
Of course, Doctor Strange as Sorceror Supreme is now without the Time Stone, but his future is his to make. The Ancient One needed Bruce to return the stone to her in order to safely put the events of the MCU movies post The Avengers (2012) into motion.
This is also why Thanos destroying the stones at the beginning of the film doesn't break the universe; for those Avengers, their future is shaped by these stones no longer being in existence. For the Ancient One in 2012, hers relies on having them still in tact so that the timelines do not splinter.