Nepal's Constituent Assembly gets 3 months extension but should Khanal resign?

A five-point deal between the three major political parties of Nepal - UCPN(M), NC and UCP-UML has extended the Constituent Assembly term by 3 months within which it is expected to pass the new Constitution. However, as reported in the news, this deal is conditional - the current Prime Minister Jhalanath Khanal has to resign for a consensus government. While the extension seems the right decision, the condition that Khanal must resign isn't.

Given the current political stalemate in Nepal, any Prime Minister before fresh elections will be a puppet Prime Minister - whether it is Jhalanath Khanal, or Madhav Kumar Nepal before him, or the next Prime Minister to be. He will not be in a position to make independent decisions. But, what is certain is that the issue of the new Prime Minister will just prolong the state of indecision and disagreement (17 rounds of elections) among the main political parties with each party vying for the PM's chair. In such a situation, wouldn't it be better to allow Khanal to continue as Prime Minister and focus on completing the Constitution write up instead?