First pauze the trace, then stop it. Stopping it will also remove the trace definition.

-- pauze trace

EXEC sp_trace_setstatus 2, 0-- sp_trace_setstatus [ @traceid = ] trace_id , [ @status = ] status

-- stop trace and remove definition

EXEC sp_trace_setstatus 2, 2-- sp_trace_setstatus [ @traceid = ] trace_id , [ @status = ] status