I suspect that this log message is not caused by the absence of the PSU but by an IOS bug (e.g. CSCuv53498 but there are more), so upgrading it may get rid of the messages.
Alternatively, configure the following to just hide the syslog messages:
logging discriminator FOO msg-body drops FRU Power Supply is not responding
logging buffered discriminator FOO
(replace "buffered" with other type of logging as required)