After the revolutions were dealt with, Franz Joseph (FJI) started centralizing his power and desired to take control of the military seeing it as an important pillar of the state and of the Habsburg dynasty itself. He was supported in this by his advisor and mentor Karl Ludwig von Grünne who was close to his mother Archduchess Sophie. This was something relatively unprecedented as the Habsburg Emperors generally stayed away from direct command, the exception to this being Joseph II.

To do that, FJI first emasculated the Ministry of War, informing it in April 1849 that he'd be taking direct control of the military including of all senior promotions and all changes in regulations.

Then he created a new office of a Personal Chief of Staff (General Quartiermeister bei meiner Person, literally 'General Quartermaster by my person') headed by Heinrich von Hess, who cooperated with Grünne and FJI in their efforts to restructure the military along the absolutist lines - a brand new Supreme Command headed by the Emperor himself and commanding 4 armies with their headquarters being in Buda, Lemberg (Lviv), Verona and Vienna. This was followed by almost constant reshuffling of the various agencies throughout the 1850s, while FJI and Grünne surrounded themselves with various adjutant officers of noble birth who were loyal albeit their military capabilities weren't very good, forming the so-called adjutant general staff (Generaladjutantur).

However, and here I will finally answer your question, in doing so they found an opposition among the most influential military commanders, namely in Haynau and Radetzky, both of whom hated Grünne and his influence on the Emperor with passion. Haynau was the easier one to deal with as he was already butting heads with Schwarzenberg, the Minister-President, over Haynau's military administration of Hungary and generally had difficult relationships with other officers. So Grünne backed Schwarzenberg and together they managed to oust Haynau who was dismissed in 1850.

Now, Radetzky was a different beast. He wasn't exactly liked by FJI, claiming that he was too 'senile' and both Radetzky and Grünne despised each other even if at least initially Radetzky cooperated with him in the matter of the military reforms. However, Radetzky was too famous and commanded too much respect and influence to be driven away in the same way as Haynau. To minimize the influence of Radetzky and hopefully induce his retirement, Grünne basically eliminated the last remaining shreds of relevance of the Ministry of War, relagating it to only routine administration duties with no influence nor participation on policy making. Moreover at the behest of Grünne FJI sent Johann Bernhard von Rechberg to Verona in 1853 to relieve Radetzky of his civil administrative duties (Radetzky was the governor/viceroy of Lombardy-Venetia) which Radetzky had no choice but accept.

Even after these events Radetzky stubbornly refused to retire, he only did so in 1857, after his health deteriorated and he died later that year at the age of 91.

Sources:

HAVEL, Petr, ROMAŇÁK, Andrej, Maršál Radecký. Vojevůdce pěti císařů, 2000

LACKEY, Scott W., The Rebirth of the Habsburg Army, 1997

ROTHENBERG, Gunther, Army of Francis Joseph, 1976

VOCELKA, Karl and Michaela, Franz Joseph I. : Kaiser von Österreich und König von Ungarn : 1830-1916, 2017