Merlin must have met with Morgan behind his back and told her about the "Pruned Event."
In the Nasuverse setting, the infinite parallel worlds could be divided into two types—
"Compiled Events" and "Pruned Events."
A "Compiled Event" was a stable world filled with possibilities, capable of developing into even more divergent branches in the future.
A "Pruned Event" was a world that had become an anomaly by deviating too far from the main route, losing most of its potential for divergence. It was judged to have reached its conclusion and come to an end, rendering further observation of its outcome unnecessary. Such a world was soon to be "harvested."
Once a parallel world was confirmed to be pruned, its operation would be halted, its potential for development severed, and every existence within it would be completely erased.
Simply put, a Compiled Event was the officially recognized main route, while a Pruned Event was the bad-ending route.
However, a Pruned Event was merely "a world that became an anomaly by deviating too far from the main route and consequently lost most of its potential for divergence." It was not necessarily a bad thing—
Take, for example, the parallel world where King Arthur and Morgan joined forces and ultimately saved Britain.
To prevent this world from being judged a "Pruned Event," Shirou had been doing his best to align with the original history.
For example, Gawain and the others' births. Wouldn't it be troublesome if half the Knights of the Round Table were King Arthur's biological sons?
Merlin had probably predicted that "if Shirou married Morgan and unified Britain, this world would develop too far from the original and meet its end."
So she explained everything to Morgan and used the grand cause of "protecting Shirou" to demand that Morgan voluntarily