I had no issues with it at all. I found it more effective than in the original, actually, as it fit with the overall character arc of Spock in the two films, whereas it was more of an isolated moment in TWOK.
My thoughts on the scream - during my downtime between my first and second viewings - was that Spock was actually sensing the approach of Khan. And the next scene does show Khan.
I was misremembering the timing of their mindtouch (which, of course, happens
afterwards), but it still works for me that Spock can sense the approach of a strong, determined mind, much as he sensed the approach of V'ger... right in the middle of his Kolinahr graduation ceremony.
So he's like the dog in
Up who constantly yells "SQUIRREL!" when he senses one nearby? And the only reason he didn't scream "Khaaaaaaaaaaaaan!" on Kronos when Khan was nearby was because Uhura had scolded him and put him in the quiet corner during their trip there? No offense, but that's pretty silly and overthinking things in the extreme.
He was pissed at Khan for killing his captain and new friend. He was pissed at Khan for killing his mentor, former captain, and friend, Pike. He was pissed at Khan for nearly destroying his ship and killing/injuring lots of his fellow crew members. He was pissed at Khan for putting his girlfriend's life in danger. He was still harboring deep anger and resentment over the destruction of his homeworld, the genocide of his people, and the death of his mother. He was confronted with a faction of Starfleet and a trusted admiral who just betrayed all of the Federation's principles and tried to kill their own people (his crew again) and start a war under false pretenses. He's an outcast among his own people for being too human and an outcast among humans for being too Vulcan.
He has a hundred reasons to be legitimately enraged at his situation, and thanks to his Vulcan upbringing, he's been taught to bottle those feelings up inside and keep them to himself, despite his human side making that more difficult and unnatural. His scream of "Khaaaaaaaaaaaaaaan!" was simply a release of all that accumulated rage and despair from what he had gone through over the past year and during the past couple of harrowing days.