@Any0day You complete narrative of the Catalyst puts somethings into perspective.
After reading everything the Catalyst said it does in a way makes sense. For the people becrying the probability and how the catalyst's absolute of it will always end in conflict. Well it said, and I quote:
"I was first created to oversee the relations between synthetic and organic life.. to establish a connection. But our efforts
ALWAYS ended in conflict, so a new solution was required."
We don't know how many times always is, nor how long the Catalyst cycle was going on, nor the repeat times the conflict broke out before a solution was required. And considering conflict did break out between the Geth and Quarians and the Quarians was nearly wiped out, saved only by the Geth not being able to reach a consensus with the ramifications of extincting their creators. And a solutions only seems to come about centuries later because Shepard needs one or both of there help against another threat, the Reapers themselves, almost implying that had the Reapers nor Shepard not been there the conflict would have resulted in extinction for one of the two races.
And again another quote:
"Reapers harvest all life--organic and synthetic--preserving them before they are forever lost to this conflict."
As I said in another thread if the organic vs synthetic conflict comes to completeness and organics are wiped out and forever lost to said conflict, thats like an organic delete. The Reapers are harvesting organic/synthetics, preserving them if you will, so that there death is not a delete but instead a back up. And then in the likelyhood of the Synthesis where organics fully integrate with synthetics/technology through their advancement (a simply likelyhood because technology exist to better our lives and the more advance the tech, the better our lives seem to become or hence the need/desire for inventions) the Catalyst states:
"and the civilizations
preserved in their forms will be connected to all of us."
And as an attempt at an analogy say you have a field of plants that have life saving properties that only can grow in that field and a fire is coming to wipe out the field and the plant, and you would do a form of reaping to preserve the plant and find a way to store it and its properties so that the fire would not destroy it completely even though you took the plant from its natural habitat/existence and placed it in an artificial construct to keep its properties/information viable.
Simply put it does makes sense its just with human/organic emotions come into play and everyone seems to see things irrationally. The only thing that can be said is "you can't harvest us like we're some kind of plant" to which a hard logical AI says "why not, I must save the data?"
"Passion rules reason,
for better or for worse. " -Wizards third rule.

Also, just to add, although it says the Crucible is little more than a power source, it also states that the Crucible changes it:
"You have altered the variables. We [can] find a new solution.
The Crucible changed me, created new... possibilities. But I can't make them happen. If there is to be a new solution, you must act."
So the little more than Power Source is little enough that it changed the catalyst and its variables and gave it new possibilities that wasn't in its original design/programming hence the option for Destroy/Control/Synthesis.
It all makes sense. Just have to think outside the box a bit.