EWrestlingNews.com has released an "early full schedule" for next Monday night's WWE RAW 1000 (which can be seen by clicking here), and one of the items on the schedule is the appointment of a new permanent RAW General Manager...SmackDown is not mentioned.
This suggests that WWE may possibly be returning to the idea of having one General Manager for RAW and one General Manager for SmackDown.
You may also recall last week that Michael Cole and Jerry "The King" Lawler were involved in a small segment on RAW where they stated who they would like to see run both brands, in which both Cole and Lawler each gave one name for RAW and another for SmackDown (Cole suggesting the Anonymous GM for RAW and Vickie Guerrero for SmackDown, Lawler suggesting Mick Foley for RAW and Teddy Long for SmackDown). This also furthers the suggestion that WWE may make this move.
Of course, plans are always subject to change, but as of this report, it appears that this may indeed be the plan.