If I saw this on an IEP, I would think the school's obligation would be to provide instructional material to the family and they would homeschool during any teacher absences. (I'm shocked it got into an IEP given that teachers can get pregnant or have an accident that could leave them out of the picture for a long while.)
It does make sense in a co-teacher situation where the odds of both teachers being out would be slim. My thought is to follow the IEP. That's the school's obligation or they will get into hot water with the state. Notify the parent to not send their child to school until your coworker is back from leave. (Let the sp ed director talk to the school's solicitor about the implications of following this clause in the IEP. It's really at this level IMO.)