Will a primary key be added as a clustered index?
Yes, SQL Server will create the primary key as clustered by default, but you don't have to accept the defaults.

ALTER TABLE dbo.foo 
  ADD CONSTRAINT pk PRIMARY KEY (bar); -- clustered

ALTER TABLE dbo.foo 
  ADD CONSTRAINT pk PRIMARY KEY CLUSTERED (bar); -- clustered

ALTER TABLE dbo.foo 
  ADD CONSTRAINT pk PRIMARY KEY NONCLUSTERED (bar); -- non-clustered


And yes, you will see some I/O activity here, so if it is a busy system, best to save this for quieter hours or a maintenance period.