Is it OK to have two record, one for the prescription being written and a second for the drug being dispensed?
No. The assumption is that a record in the drug table is the best estimate that a person received treatment. You already identified the problem, having records for both prescribing and dispensing will give misleading results. From your description, you will get a notification when the drug is dispensed, that is what should be recorded in Drug Exposure.
Your use case:
’ We would like to store in OMOP CDM both, prescribing information as well as dispensing information.’
is not something the OMOP CDM is designed to handle. You would not be the first to request an Orders table to hold this type of information. Also, it is not a violation of OHDSI standards to add columns or a table for local needs not supported by the CDM, so you could add a Prescription table.
The Fact_Relationship table is for maintaining one to one relationships between entities in the CDM.