Here are some revealing tidbits about Magruder regarding the factors behind his transfer to the Trans Mississippi.

This may clear up some popular misconceptions about Magruder being sent to the dumping ground by Lee.

It is also interesting to note that his original Trans Mississippi assignment was as commander of the Trans Mississippi district [or Department as Magruder calls it].

Confederate Tide Rising Joseph Harsh
Appendix Five
C. Lee and the Replacement of Huger, Holmes, Magruder and Whiting
....Magruder had been assigned to the Trans-Mississippi on May 23, a week before Lee replaced the wounded Johnston, but the order had been temporarily suspended and was reinstated at Magreduder's own request.

R. E. Lee: A Biography by Douglas Southall Freeman
Magruder, brave and loyal for all his pompous manner, was too excitable for such fighting as lay ahead. Fortunately, the question of disposing of him had been solved in advance: he had been offered command in the Trans-Mississippi department, was anxious to go there, and waited only long enough to defend himself against whispered imputations of poor generalship at Malvern Hill121
121 O. R., 11, part 2, p674 ff., ibid., part 3, p630; O. R., 13, 845.

And from the Official Records:

SPECIAL ORDERS, ADJT. AND INSP. GENERAL'S OFFICE,

Numbers 118. Richmond, Va., May 23, 1862.
VII. Major General J. B. Magruder is assigned to the command of the Trans-Mississippi District, of Department Numbers 2, and will report to this office for instructions.

HEADQUARTERS CENTRE, Battle-field at Crew's Farm, Va., July 2, 1862.
Honorable GEORGE W. RANDOLPH,
Secretary of War:
SIR: The enemy having now changed his front and being driven to a new line, on which (should he attempt further movements against Richmond) time indefinite in its duration will be required for the execution of his plans, I consider the period has arrived when I cannot with propriety ask the longer indulgence of the Government in respect to the order already assigning me to the command of the Trans-Mississippi Department. I have the honor, therefore, to announce my readiness to conform to the orders of the Government relative to my new position as soon as they may be communicated to me.
Very respectfully, your obedient servant,
J. BANKHEAD MAGRUDER,
Major-General, &c.