Christopher Marlowe wasn't killed but banished...

 Marlowe Lives!
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Document proves Marlowe was a valued agent of the Queen (1587)

In 1587, after 7 years of study, Marlowe was denied his Masters degree by authorities at Cambridge University  because he had not been resident on campus for the length of time required. (He had missed several weeks.) This was during the height of the so-called Babington plot against Queen Elizabeth, and master spy Robert Poley helped orchestrate an elaborate ruse that ultimately would result in the execution of 14, including Mary, Queen of Scotland. This same Robert Poley was reportedly with Christopher Marlowe during the poet's final hours and claims to have witnessed his murder.

The note of the Privy Council to Cambridge University authorities makes it very clear that Marlowe was a highly valued agent.

Privy Council note on Marlowe's behalf to Cambridge University

Whereas it was reported that Christopher Morley was determined to have gone beyond the seas to Rheims and there remain, their Lordships thought good to certify that he behaved himself orderly and discreetly whereby he had done her Majesty good service, and deserved to be rewarded for his faithful dealing. Their Lordships request that the rumour thereof should be allayed by all possible means and that he should be furthered in the degree he was to take this next Commencement; because it was not her Majesty's pleasure that anyone employed as he had been in matters touching the benefit of his country should be defamed by those ignorant in the affairs he went about.

Marlowe Lives!