Clemenza was absolutely, totally loyal to Michael. There was no reason for Michael to whack him--none.
BUT:There are many script anomalies in the Trilogy, and some of them create the doubts and possibilities expressed in this thread. First, we have Willie Cicci claiming to Fredo that Clemenza's death "...was no heart attack." Later, in the boathouse, Michael says to Frankie, "Clemenza promised the Rosato brothers three territories in the Bronx after he died...he died, you didn't give them to them." Frankie replies, "Clemenza promised them ugaz...he hated them Rosatos more'n I did."
How explain these differences? Clemenza, as head of the NY "olive oil business," was subordinate to Michael, though I assume Michael kept him on a fairly loose leash. Michael may have pressured Clemenza to give the territories to the Rosatos as a favor to Roth. Clemenza may indeed have hated the Rosatos, but rather than go against Michael, he offered a compromise: the Rosatos could have the territories after he died. Frankie took over, and was trying to get out of the deal by questioning Clemenza's sincerity.
As for "that was no heart attack," I'm guessing it was just a figure of speech that Cicci used to reinforce his and Frankie's position that the Rosatos were bad guys. The probable real reason is sloppy scriptwriting.
As Olivant and DC alluded, the Frankie/Rosatos conflict is based on a real-life NYC Mob story:
Around 1959, Frankie (Shots) Abbatemarco, a small-time gangster, opened some gambling joints in territory belonging to Joe Profaci, one of the original Dons made by Salvatore Maranzano after the Castellemmarese War. Profaci demanded tribute, Shots refused. So Profaci ordered a faction in his family, the Gallo brothers (Larry, Crazy Joe, Albert "Kid Blast") to kill Shots. Profaci promised that he would give the Gallos the gambling joints that Shots operated after they did the job.
The Gallos arranged for Shots' murder. But Profaci welshed--he didn't give them the gambling joints. So the Gallos kidnapped several high-ranking Profaci bosses, and narrowly missed getting Profaci himself. They held them hostage. Profaci called for a meeting of the Commission. The Commission ordered the Gallos to release the hostages, and Profaci to give the Gallos what he'd promised them. The Gallos complied--but Profaci welshed again. This time the Gallos seceeded from the Profacis and started a war. As DC wrote, Larry Gallo was lured to a meeting in a Brooklyn bar and was garrotted by Profaci men, but survived because a policeman happened by and broke it up. The war petered out after Profaci and Larry Gallo died of cancer, and Crazy Joe went to prison for a decade on racketeering charges. Joe Magliocco, Profaci's brother in law, took over the family. He conspired with Joe Bonanno to whack Carlo Gambino and Tommy Luchese. The plot was betrayed by a Profaci captain, Joe Columbo. The Commission forced Magliocco to apologize, pay a fine and step down. Columbo took over the Profaci family. The Commission demanded that Bonanno explain his role. When Bonnano refused, the Commission "removed" him as Don and put Gaspar DeGregorio in his place. This started another war--and another story.