Fix some random test failures following MDEV-32168 push.

Don't blindly set $rpl_only_running_threads in many places. Instead explicit
stop only the IO or SQL thread, as appropriate. Setting it interfered with
rpl_end.inc in some cases. Rather than clearing it afterwards, better to
not set it at all when it is not needed, removing ambiguity in the test
about the state of the replication threads.

Don't fail the test if include/stop_slave_io.inc finds an error in the IO
thread after stop. Such errors can be simply because slave stop happened in
the middle of the IO thread's initial communication with the master.
Signed-off-by: Kristian Nielsen <knielsen@knielsen-hq.org>