Would Dr Hannibal Lecter allow himself to be a consultant with Clarice if Miggs hadn't behaved improperly to her?

It's not clear, either from the script or the source novel what Lecter's motivation for engaging with Agent Starling was, but we do know that Lecter has been planning an escape for some considerable time. He clearly sees the visits he's been receiving (from Clarice, Jack Crawford and various other unnamed psychologists) as a potential source of material for his needs.

It strikes me as highly likely that he'd want to encourage future visits from Clarice, who he sees as quite skittish and hence more prone to making mistakes. Obviously the best way to do this is to give her a good reason to return:

In all the years after he savaged the nurse in the Baltimore asylum, there had been only two lapses in the security around him, both on Barney's days off. Once a psychiatric researcher loaned him a ballpoint pen and then forgot it. Before the man was out of the ward, Dr. Lecter had broken up the plastic barrel of the pen and flushed it down his toilet. The metal ink tube went in the rolled seam edging his mattress.

The only sharp edge in his cell at the asylum was a burr on the head of a bolt holding his cot to the wall. It was enough. In two months of rubbing, Dr. Lecter cut the required two incisions, parallel and a quarterinch, long, running along the tube from its open end. Then he cut the ink tube in two pieces one inch from the open end and flushed the long piece with the point down the toilet. Barney did not spot the calluses on his fingers from the nights of rubbing.

Six months later, an orderly left a heavyduty paper clip on some documents sent to Dr. Letter by his attorney. One inch of the steel clip went inside the tube and the rest went down the toilet. The little tube, smooth and short, was easy to conceal in seams of clothing, between the cheek and gum, in the rectum.

No, even though Hannibal Lecter feels bad about the way Miggs behaves and kills him by messing with his head. Lecter was desperate to get human attention after all he is a professor who delivers speeches on mental behaviors.

• he was able to profile the FBI agent and decide she is innocent
• he recognized the pattern of the serial killer and was able to link it back to his patient
• he knew about the island, which was fake and knew he could not get a better deal than the FBI agent for interaction

I agree that it is not clear, but Thomas Harris choice to write Hannibal (following novel) the way he does, and then Hannibal Rising does at least make us understand or better speculate a few things>

1. The reason Clarice becomes important to Hannibal is because he tragically lost his little sister Misha (Hannibal Rising) and during the course of Hannibal (novel), we learn he is trying to alter or transform Clarice so that his sister's conscious can reside in Clarice's body--she is meant to be a vessel...
2. There are similarities between thee Clarice of Silence of Lambs to Mischa in the sense that Clarice is not meticulous or concerned much with her appearance. Hannibal's sister being under the age of five when she dies, was also not meticulous, or elegant, or overly concern with her identity. So It's easy too see what Hannibal initially saw in Clarice---a sister to teach. And then of course Clarice and Hannibal both have tragic upbringings, which also bonds them.

Bryan Fuller's adaptation/prequel really borrows a lot of conceptual ideas from the novels, and began to incorporate some magical realism elements to better flesh some of it out. Will Graham sees "time in reveres" a direct reference to the novels with Hannibal's obsession with Stephen Hawking (Brief History of Time). I almost suspect he would have, should the series have gone on, filled in some things between the seven year gap between SOTL and Hannibal that the novels do not fully disclose. Potentially he may also have expanded on the idea of Hannibal coming to believe that Clarice could be a "vessel" by having Clarice be "clairvoyant" or something, because even the idea of him wanting to use her in such a specific way, is not disclosed--in part because the mystery of it helps feed into both characters' transformations at the end of the novel, as basically Harris is saying, that perhaps, Love conquers all.