Yes, it would. Because nothing up to that point in the series had mentioned Heracles, Zeus or the White Guardian; there had been no hint at either their existence, or their having the ability to pull off such a feat.
By contrast, it had been firmly established that a) Amy had spent her whole life in direct proximity to the crack (evident from the very first episode), b) this had had huge consequences on her life (hinted at over the course of the series and made explicit in the final episode), c) this unique position had resulted in a powerful link between her and the time vortex, sufficient to recreate portions of the universe from nothing (this being the reason that Rory was able to return as more than a mere automaton in the penultimate episode), d) that the logic behind the cracks' modifying the universe was affected by highly subjective factors (it made things 'not have happened', but only parts of the consequences were actually removed, blatant inconsistencies resulted, and whether memories were erased or not could depend on how 'important' they were), and e) that the Doctor was not even strictly speaking 'gone', merely trapped on the other side of the cracks.
Based on these established facts, it seems entirely feasible that Amy remembering the Doctor could bring him back. The cracks' rewriting of the universe was imperfect; they just wiped from history anything that they 'absorbed', erased the most obvious consequences, and wiped memories to make things seem superficially consistent. The Pandorica's light directly reversed this effect, latching on to anything that had been imperfectly erased and fully restoring it. When this light was spread through the cracks themselves, reaching the entire universe just as the cracks did the same, it basically cancelled them out and restored the universe, removing all the inconsistencies with the exception of one: the Doctor himself (and the Tardis) were not restored, because they were at the centre of it all, right inside the cracks, outside of the universe.
As such, the cracks' logic persisted around that one point: all obvious consequences of the Doctor's existence were removed, and everyone's memories of him were wiped. They gave the world a superficial 'consistency' that did not include the Doctor. However, Amy remembering the Doctor caused that superficial consistency to break down. Perhaps ordinarily, one person remembering wouldn't be enough to actually bring him back, but as the person in question was Amy, wih her powerful connection to the whole phenomenon, it was enough to restore some measure of connection between the Doctor and the universe - and I'm guessing that the Doctor himself, was able to take advantage of that connection to transport himself out of the limbo he was trapped in, and back into the universe proper.
Now, this is just my understanding of the whole thing, and I'm not claiming that it's the only possible interpretation. I'm not saying that there aren't perfectly reasonable complaints you could make, either. I could understand, for instance, if you weren't happy with Amy's lifelong proximity to the crack giving her such a profound connection to the time vortex, or if you didn't like the idea that the Pandorica could have such an all-powerful restorative ability. But neither of these complaints make the conclusion deus ex machina, because deus ex machina come out of nowhere, whereas these factors had been hinted at and established ahead of time.