I gotta go with Jack on this one as it's a rather simply case of appropriately heading-off the area where the toilet drain lines are located. Happens all the time and I don't care how careful one does their layout because the WC's drain flange will always land on top of a floor joist, Murphy's Law you know. That's also the reason plumbers are equipped with chain saws.

Is a structural engineer over kill? Probably, but if you do not use a structural engineer, you may get a contractor who knows what they are doing and can 'do the job right', or one who does not know, or care, what they are doing and does 'whatever', then, either way, you end up with a repair and no one to back up its integrity - hence the need for the structural engineer anyway.