The whole thing started with the Milala and was only later corrupted and refined by Preservation, but even if we ignroe this and just look at real fusion itself, it's original intended purpose still does not make it inherently evil and impossible to use for good.

The Garlean war machina were developed to conquer and subjugate the world and yet we and others used some of them to fight back agains the Garleans, and later the Garleans used their makina to safe people from blasphemies.
There's also a good chance that airships in general were first and foremost developed as military vessels by Garlemald and yet we all love the Enterprise and nobody would consider her evil.
We used parts of Dalamud to upgrade the engines of the Ragnarok, so we could get to Ultima Thule.
Omega was designed to wipe out other civilizations, and yet we didn't only use it fight Shinryuu to a stand-still, but eventually even managed to turn it around into... well, at least a neutral, non-hostile party, if not exactly a friend or ally.

Again I did not decide anything, I asked a question. Is is possible? Is there a scenario, where it makes sense?
Obviously it should not be done, just because it can be done and would only be a last resort, if all attempt to stablilize the shard in question fail.

There's also the Void and the First to consider. We already had one instance of pulling light aether from one to send to the other, so we already have a kind of proof of concept of dumping one's excess aether into the other is possible and having apparently a positive effect on both. Realm fusion might be a way to do this in a way that more directly connects the two reflections, without the complication of having to utilize the Tower of Babil, the Crystal Tower and the seals that once held Zodiark, to keep an accidental void-sent incursion from happening.
Again, I'm not necessarily saying it can or should be done, but I think it's worth thinking about, or at least fun to speculate a little bit.