You can do it from above...just don't fall through!
The biggest things are maintain the proper slope, keep the venting working properly, and don't compromise the strucure.
Depending on whether you have 3 or 4" waste line for the toilet can vary what you do. Trying to maintain slope when moving with 4" can be a big challenge since the bends are deeper than available with marginal joists.
If the pipe is 4", it's easier since you can use an internal flange - just run the pipe high, install the subflooring, then the finished floor right up to the pipe, then install the flange after cutting the pipe to the proper height. If it is 3", you need to leave a space around the pipe to allow the flange fitting to slide over the outside of the pipe. If you didn't catch this - the proper position of the flange is the TOP of the FINISHED floor, not on the subfloor