Marlowe's option would have been to find another front man to take on the "Shakespeare" role, which admittedly would have been much easier earlier in the scam than later when WS's reputation had been built up. If you need to keep using Shakespeare as a front, you'd find a way to announce that WS had gone on a long trip to the ends of the earth, but the works keep being sent back for publishing at intervals. So, there'd be ways.

As far as working out the split, a moral person would have offered WS a good enough severance package that it was in his interest to keep his mouth shut...while an unsavory one would make him 'an offer he can't refuse' or just arrange for him to meet an untimely end and disappear.