I would actually have been comfortable with the psychic block thing had it been qualified in a different context, making it appear that Xavier did it only as a last resort.
The emergence of the Phoenix (and Dark Phoenix) in the films could have been explained as a confluence of several factors: (Just my two cents)
1) The natural development of Jean's awesome powers was stunted as a result of mental blocks which Xavier put in place (not to cage her but to keep her from going nuts) to shield her mind from the pain of a traumatic event she encountered early in life (perhaps much like in the comics).
2) With Xavier's tutelage and ongoing therapy sessions, the adult Jean had achieved some skill in controlling her powers and gained a somewhat balanced sense of self (although much work still had to be done in both cases).
3) Since things were going pretty well, Xavier decided to allow the mental blocks to come off once Jean became psychologically prepared to face the ghosts of her past.
4) Jean's use of Cerebro in X1 unexpectedly uncovered memories of her childhood trauma and quickly unraveled thoughts and feelings about her true self/potential that were otherwise buried deep in her subconscious, thus causing confusion and some mental instability.
5) Her exposure to Magneto's machine exacerbated the situation in that it brought to the fore her once suppressed powers in a much more accelerated pace, causing her to lose further control of her abilities, which in turn, added in her the sense that she was "losing it."
6) As if these developments weren't enough, in comes Logan trying to seduce Jean. While feeling some sort of animal attraction for him, thus, flirting with him on occasion, Jean knew deep in her heart that Scott was the man for her. Hence, she became "torn between two lovers" -- a man she wanted to spend the rest of her life with and a manimal she liked to try out in bed just for kicks. Such repressed feeling, which stems from one's "id" -- the cesspool of instincts and desires -- which drives ordinary humans to great heights of passion and creativity, is actually the fuel that drives her Phoenix-like powers to peak (think of orgasm, if you will).
7) Having walked the path of the straight and narrow all her life, Jean was slowly, albeit unconsciously, starting to tread on the wild side, thanks to Logan, and a part of her liked it. At the same time, though, she felt a strong sense of guilt for not being totally faithful to the guy she loved and was commited to. Thus, her personal conflicts continued to multiply as she was getting more in tuned with her "Phoenix" self.
8) Being unable to comprehend the changes in her in relation to her powers, as well as, the nightmares which pointed to her past and the darkness she foresaw which she sensed she will play a great part in, Jean, now fully as the "Phoenix" decided to sacrifice "life" and personal happiness to "go away" temporarily at the end of X2 to sort things out in solitude.
9) Still, her heart ached for Scott and knowing the pain she must have caused him, she constantly called out to him in his dreams. Scott, though, instead of reaching out for support in his bereavement, further isolated himself and became aimless, bitter, and angry.
10) In a parallel development, Magneto was able to recruit a powerful telepath (Psylocke, maybe) and empath (Emma Frost, as envisioned by Bryan Singer) to his cause. Together, these two sensed the very strong internal turmoil brewing in Jean's psyche but did not truly believe it was her since they were told that she had already perished. They tried to track her down to make sense of it, nonetheless. Sensing that Xavier had also felt the same thing as they did (which was just a confirmation of his earlier feelings of Jean still being alive) and was hot on their trail, they decided to psychically incapacitate him for a while for some lead time. As they approached Alkali Lake, they witnessed the fight that was about to take place...
11) Scott, in a fit of anger, convinced that he was merely hearing voices in his head, released a very powerful optic blast into Jean's watery grave.
12) Not knowing what hit her, Jean, now stronger than before, burst from her telekinetic cocoon and, as if relflexively in an act of self-defense, unleashed a torrent of psychic bolts onto her "attacker."
13) As things settled down and Jean came to her senses, she realized that she had unwittingly "killed" Scott. This became another major trauma for Jean, one that approximated her childhood one in scale, and put her in a semi-catatonic state.
14) The Brotherhood came in and secured Jean. They seemingly nursed her back to health while fed delusions to her extremely volatile mind such as: (a) She would not have felt so incomplete all her life had Xavier not manipulated her, (b) She could have achieved so much greatness on her own, (c) Without Xavier, mutants could have been the superior race in humanity, (d) Like her, Scott was merely a victim in the broad scheme of Xavier's machinations therefore Xavier was also to blame for his "death", (e) If Scott only had the "balls" the same way Logan did, he would not have been an unwitting tool in Xavier's quest to subdue her powers, and so on and so forth. All of these prompted Jean to question reality and her feelings of loyalty and fealty turned to pure rage.
15) All of the foregoing developments tipped the scales so to speak, which gave rise to the extremely mad, extremely crazy, "Dark Phoenix."
16) IMO, X3 or X4 should've been about the quest to rescue Jean and her inner struggle to redeem her sanity, to free herself from her past, and for letting the Phoenix within her truly rise from the ashes.