I would like to know if there is a Resource I could use to represent medication alternatives, such as:
If you are taking Drug A , you should use Drug B or Drug C instead
This is not something that FHIR has implemented yet - it's clinical/medical knowledge. The nearest that FHIR currently has is the Clinical Quality Framework: http://hl7-fhir.github.io/cqif/cqif.html
Warning: It's very much a work in progress, and the link above is to the current build, not a stable release