Is it ever harmful to set a database owner in SQL Server?
You should be using DDL instead of backward compatibility stored procedures:

ALTER AUTHORIZATION ON DATABASE::dbName TO sa;


And the owner of the database (never mind sa) should probably not be the account that your applications use, so this should not really have any effect on your applications. If it does then you should update the connection strings your application uses (which shouldn't be a major change) and make sure the account has sufficient - but not God - privileges.