Despite the positive impact, Munshi Sahib faced opposition from communist elements within the Writers Guild, who clashed with writers and poets of Islamic perspectives. These factions were disturbed by Munshi Sahib's secretaryship and frequently conspired against him. Through constitutional means, Munshi Sahib thwarted their schemes and united patriotic and Islamic-minded writers, preserving the integrity of the Guild for four years while advancing its literary cause.​

Due to the conflicts and controversies affecting his reformative and literary efforts within the organisation, Munshi Sahib resigned from the Pakistan Writers Guild. The Daily Nawa-e-Waqt Lahore commented on his resignation, stating:

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“Munshi Abdul Rehman Khan deserved to be congratulated that instead of surrendering before communist writers he fought against their conspiracies and foiled their designs. This is infact duty of every patriot and Islam loving writer and author to help achieve this great task. 

Writers Guild had become an asylum and sanctuary of the communist minded writers and poets of not only Multan but of the whole country. So much so that the elements who were previously active in furthering their agenda through communist party, NAP, Anjuman Taraqqi Pasand Musannafeen and similar organizations were now using the platform and cover of Writers Guild for their communist activities. In each area they were establishing communist cells as they considered themselves safe under the shelter of Writers Guild. Meanwhile there was also a group of good natured but simple and innocent people who were unaware of the communist tactics and misled by assumption that they would utilize the communist writers for the greater good of the country.

Although nowhere in the world non-communist people have ever succeeded in using communists for achieving personal national or state objectives. These are the communists who have capitalized over the simplicity and good nature of non-communist and use them. We have already started experiencing dangerous results of this lax attitude. Communists in the name of art and literature have succeeded in establishing their cells in several universities, colleges, Arts Councils literary bodies, Radio, T.V and Print Media. Infact In non-communist countries the first target and objective of communist parties have been to capture sources and institutions of mass communication, literature and education. The same had been happening in Pakistan and results were before us. 

There was a need that not only in Multan but all over Pakistan conspiracies and subversive activities of such elements be confronted with full force."

Munshi Sahib's resignation marked the end of a significant chapter in the Pakistan Writers Guild, highlighting his dedication to preserving literary integrity against ideological subversion.