I'll try to answer all of your questions since they are mostly related:
Is there any evidence that midi-chlorians are disturbed by imbalances in the Force?
It appears that in the view of the most powerful direct manipulator of midi-chlorians, that they indeed are disturbed by balances of the Force. The most clear discussion of how midichlorians work is found in the novel Darth Plagueis, which is one of the last Legends novels.
One passage does seem to indicate that (at least in Plagueis' view) the midichlorians do have an idea of imbalances in the Force, and the capability to act in response: (p. 279 of the hardback edition):
[..] Almost a decade earlier, they had succeeded in willing the Force to shift and tip irrevocably to the dark side. [..] The shift had been the outcome of months of intense meditation, during which Plagueis and Sidious had sought to challenge the Force for sovereignty and suffuse the galaxy with the power of the dark side. Brazen and shameless, and at their own mortal peril, they had waged etheric war, anticipating that their own midi-chlorians, the Force's proxy army, might marshal to boil their blood or stop the beating of their hearts. (emphasis mine)
The passage goes on to say how Plagueis goes on to increase his ability at repairing injury with the force by manipulating midichlorians, over and over allowing a test subject to die and reviving him. Plagueis then goes on to heal his own body and slow his aging.
Drunk on newfound power, then, he had attempted an even more unthinkable act: to bring into being a creation of his own. Not merely the impregnation of some hapless, mindless creature, but the birth of a Forceful being. [..] But ultimately to no end. The Force grew silent, as if in flight from him, and many of the animals in his laboratory succumbed to horrifying diseases.
I would present this as evidence that Plagueis, for good reason, saw the midi-chlorians as making concious choices to 'balance' the Force in opposition to his work.
Could they have created the prophecy of "The Chosen One" and also inspired/forced Darth Plageuis to create the one that would bring balance to the Force?
All these events take place before the events of Episode I, but towards the end of the novel we come upon scenes from the film, from a different point of view, when Dooku relays to Palpatine the discovery of Anakin Skywalker. (p. 346):
"Qui-Gon returned from Tatooine with a former slave boy. According to the boy's mother, the boy had no father."
"A clone?" Palpatine asked uncertainly.
"Not a clone," Dooku said. "Perhaps conceived by the Force. [..] born into slavery nine years ago" [..]
Palpatine had stopped listening. Nine years old...Conceived by the force...Is it possible...
Plagueis is struck by the same thoughts at the news.
He had to see this Anakin Skywalker for himself; had to sense him for himself. He had to know if the Force had struck back again, nine years earlier, by conceiving a human being to restore balance to the galaxy.
Darth Plagueis was not inspired or forced to create Anakin, he was shocked by Anakin's existence, and even at the height of his powers, was unable to create life himself. As to the origins of the Chosen One prophecy, that's an entirely separate and unrelated question. As to the title question, it appears that, yes, the midi-chlorians did indeed create Anakin.
Do the events of the prequel take place simply because the midi-chlorians are uncomfortable with an unbalanced Force?
I'd encourage you to read Plagueis - in my opinion, it's the finest of the pre-Clone Wars/Clone Wars EU novels, and it really fleshes out the machinations done to bring about the various crisis's of Ep I-III. But overall, I'd say no, Anakin's existence certainly brought about major changes to the events, but he did not cause them.