During a brisk ebb flow there is more turbulence around the island than at slack or flood. You can use the same direct route shown on the slack and flood section; this is the "just row through it" approach. However, consider the following alternative, if only for the discussion of the rough patches you may find otherwise.
Counter clockwise around the Island (if you arn't concerned with wind through the GG you may want to go around the other direction; see the end of this section):
If you follow the direct path from the Sausalito channel to Pt. Knox you will row parallel to good sized swells (if the ebb is significant) formed as water rushes out of Raccoon St. into the larger part of the bay. If there is a breeze through the Golden Gate against the current (as there often is, especially in the summer) the swells become steeper, eventually developing white caps.
It is longer, but can end up being faster and more pleasent, to first row to Belvedere Pt., inside of the Green 3 buoy. Here stop, turn around, and look at the water between you and Angel Is.
If it is smooth to the North, but rough to the South (toward the Golden Gate) row up into Raccoon St. slightly, and curve around to pass between Red 4 and Pt. Stuart. If it is rough to the North, but smooth to the South, follow the dashed path instead. As you row out into the current you will be carried to the South, but don't try to compensate completely, just row as hard as you can. About halfway across you should get into a counter current which will carry you back to Stuart Point. The first half of the Raccoon crossing will be the roughest. Rowing across the little cove between Pt. Stuart and Pt. Knox will be a pleasure.
There is an important and very general suggestion above: there are times and locations where you should carefully examine the water around you in order to plan your route. It's hard to see the condition of the water when you are so low, but it can be so useful that you should practice looking anyway, and improve your powers of observation by comparing the conditions you find with those you predicted.
The row down the island to Pt. Blunt should be uneventful, but there is often a significant current parallel to the island if you are more than 50 m out. It shouldn't be rough going into Pt. Blunt, but the ebb current flowing down the East side of the island will be quite rapid if the ebb is strong. Thus, stay close to shore as you round Pt. Blunt.
Pt. Blunt not a good place to fall out of your boat. The rip that forms beyond buoy 3, as the current flowing South meets current flowing North, is arguably the roughest patch in the Bay.
There will be a good counter current flowing up the shore of the cove, so it is well worth the little extra distance to stay close to the shore until Quarry Pt. At Quarry Pt. you will find a swift current, but it's usually not rough. Rowing close along the shore of the shallow cove to Pt. Simpton doesn't seem to gain you much, perhaps because there is no up stream barrier, the current just extends into the shore. There can be very rough water off Pt. Simpton, but it's erratic in time, on and off every few minutes. The current around Pt. Campbell can be very difficult. It's almost 200 ft deep just North of the Point, but there is a shelf only 20 ft deep around the Point. The ebb current flows up into this shallow shelf with impressive results. You probably don't want to get too far from the shore, because it is very rough. However, if you get too close to the rocky shore you risk beaching the boat as the erratic swirls turn you first one way and then another. You pick the compromise.
Now at least you are rowing with the current. If timid, row along the shore and cross where you did before. Otherwise you can take a sleigh ride down the middle of Raccoon St. to Belvedere Pt. and back to OWRC.
You will want to avoid as much as possible of the ebb flow through Raccoon Str. by rowing to Belvedere Pt. and then crossing quickly. See the previous section on rowing around CCW to decide how to cross. When you cross and are close to buoy Red 4 you should pick up a counter current. Once you get to the E side of the Island you will have a nice ride down to Blunt Pt., and the row up the S side of the Island should be uneventful. When you pass Knox Pt. you should look at the water and decide if you need to go up to Pt. Stuart to avoid swells to the South, or if you can just row directly to the OWRC.