The problem is that we've never seen a Rejoining happen that doesn't involve an entire world's worth of beings being killed. The problem with Rejoinings are not the Calamities. The lives lost in a Calamity are small potatoes compared to the lives lost when a Shard's aether is collapsed into the aether of the source. We've also seen that Hydaelyn views the lives on the Shards as being as precious to her as lives on the Source are. The entire reason Solus is viewed as being wrong is ShB is that the WoL and the Scions view all life as being worth saving, no matter how "partial" that life is. A Rejoining fundamentally results in life being destroyed.

As a side note, the Shards are not like... other Continents that can just be grafted onto the Source. They are exact replicas of the Source that occupy the same "space" as the Source does, just at a different "dimentional frequency". When a Rejoining happens, the Shard still occupies the same space as the Source does, but as aether on the same "dimensional frequency" of the Source. The very reason why the Source is called the Source is that it is the original dimension everything else is based on and therefor is never destroyed when a Rejoining happens. The other Shards always are.

We also don't know if Hydaelyn really is the one keeping the Shards sepprate from the Source. It could very well be the case that killing Hydaelyn would not change how the Shards and Source function.