I was thinking about this earlier....
I THINK (I'm at work, can't check) there is a place in S3D to put gcode between layers. If you slice in makerware and export the gcode, you can go find the place where it does the wipe walls. you could (after much work and hard thinking and all kinds of other "it's on you if it goes wrong") copy that code, throw in any changes that would be more condusive to S3D and put it in between layers. If you didn't want to copy the gcode, you could also model the walls and slice them in S3D and put THAT code in, though I think they're doing some ninja stuff on extrusion towards the end of the walls, so it's not likely to give you the same effect if you just slice in S3D.
Something to think about. Since Makerware still manages to pump out gcode, the magic is all there for your benefit.
The only thing I'd explicitly warn about (that I can think of right now in my head on a moment's notice) is that you'd want to pull the gcode from a test file in makerware where you'd almost completely filled the plate. You'd want those wipe walls far away from any print since they would be positioned absolutely regardless of where your main print was.