Even so, I doubt that the Overmind would've been able to create Xel'Naga through this process because it can be later argued that the Overmind was under DV manipulation such that the assimilation would've instead created Hybrids.
That problem you've mentioned is the beginnings of another plot-hole. From what we have said so far, the Overmind must die and at some level, must know this in order to achieve it's goal (propping Kerrigan up in its stead). That means the only real reason it goes to Aiur is to die, but how does it know that that is exactly going to happen? I've mentioned something to this effect in another thread about this because this inference means the Overminds 'plan' is a "Xanatos roulette" (a plan that relies on conditions that the planner cannot take stock of and control yet comes off without a hitch exactly as the planner had wanted). It kinda got debunked because there wasn't enough evidence that the Overmind was really planning anything - Kerrigan's infestation and whatever happened next (becoming saviour and all) was just unforeseen and extremely fortuitous for the Overmind (I cried BS at the validity of this "extremely fortuitous" part - there is only so much suspension of disbelief one can have afterall and at that point, to me it seemed like it was not only taking the cake and eating it, it was digesting it and shitting it out, too ). Also, this is not mentioning how the directive is seemingly ok with such an idea (its nebulous influence seems rather quaint - it seems to be able to push the Overmind into doing some things but not others, like not trying to commit suicide for instance...). Whether the Overmind planned, expected or wished the sequence of events that have happened to 'prop up Kerrigan', the whole thing still feels like a big stick-in-the-mud.