Well, there are really only two possible cases. Either Crucible is a better solution than the cycles, or not. If it is, Catalyst could have built it by itself. If it is not, Catalyst shouldn't have let Shepard use it. Either way, the ending makes no sense.
There is another possible case, that Crucible is actually a threat to Catalyst, but it just finally saw that it couldn't prevent its creation eventually. Still, if Catalyst managed to prevent its construction for hundreds millions years, there is no reason to believe it won't prevent it for hundreds millions years more.
Catalyst explained all this by a "new variable" coming from event that seemed impossible to it. How come such an advanced intelligence couldn't predict creation of the Crucible? Organics managed to build it from scratch in a few months while being exterminated all over the galaxy, and the most advanced intelligence in the world couldn't predict it in a billion years?
So I don't go away from my claim: Catalyst's software had a few bugs in it. Its logic doesn't make sense, but perhaps the programmers simply wrote "mov ax, bx" instead of "mov ax, cx" somewhere?