This functionality isn't built into the tool, but you can do it pretty easily. Let's say that you want 100 points total, 50 points in each strata. First, use the Create Spatially Balanced Points tool with your binary raster, and create 50 points. Then, use the Raster Calculator in Spatial Analyst to switch the 0's and 1's of your raster; the code will be (1 - "value"). Then create 50 more points with the new raster. You'll now have two point feature classes, each with 50 points, and they'll each be within a different strata. You can then combine them into a single feature class using the Append tool.
Let me know if you have any questions.