tmux configuration stanzas based on Tmux version

Is there a method by which I can suppress this output?

Yes. The set-option and set-window-option commands take a -q ("quiet") flag, which suppresses errors about unknown options. This should cover you:

set-window-option -gq mouse off
set-window-option -gq mode-mouse off
set-option -gq status-utf8 on
set-window-option -gq utf8 on

Based on @ericx's answer and @thiagowfx's answer I put the following together which covers the listed incompatibilties from version 2.0 onwards:

# Version-specific commands [grumble, grumble]
# See: https://github.com/tmux/tmux/blob/master/CHANGES
run-shell "tmux setenv -g TMUX_VERSION $(tmux -V | cut -c 6-)"

if-shell -b '[ "$(echo "$TMUX_VERSION < 2.1" | bc)" = 1 ]' " \
    set -g mouse-select-pane on; set -g mode-mouse on; \
    set -g mouse-resize-pane on; set -g mouse-select-window on; \
    set -g message-fg red; \
    set -g message-bg black; \
    set -g message-attr bright; \
    set -g window-status-bg default; \
    set -g window-status-fg default; \
    set -g window-status-current-attr bold; \
    set -g window-status-current-bg cyan; \
    set -g window-status-current-fg default; \
    set -g window-status-bell-fg red; \
    set -g window-status-bell-bg black; \
    set -g window-status-activity-fg white; \
    set -g window-status-activity-bg black"

# In version 2.1 "mouse" replaced the previous 4 mouse options
if-shell -b '[ "$(echo "$TMUX_VERSION >= 2.1" | bc)" = 1 ]' \
  "set -g mouse on"

# UTF8 is autodetected in 2.2 onwards, but errors if explicitly set
if-shell -b '[ "$(echo "$TMUX_VERSION < 2.2" | bc)" = 1 ]' \
  "set -g utf8 on; set -g status-utf8 on; set -g mouse-utf8 on"

# bind-key syntax changed in 2.4 -- selection / copy / paste
if-shell -b '[ "$(echo "$TMUX_VERSION < 2.4" | bc)" = 1 ]' " \
   bind-key -t vi-copy v   begin-selection; \
   bind-key -t vi-copy V   send -X select-line; \
   bind-key -t vi-copy C-v rectangle-toggle; \
   bind-key -t vi-copy y   copy-pipe 'xclip -selection clipboard -in'"

# Newer versions
if-shell -b '[ "$(echo "$TMUX_VERSION < 2.9" | bc)" = 1 ]' " \
   bind-key -T copy-mode-vi v   send -X begin-selection; \
   bind-key -T copy-mode-vi V   send -X select-line; \
   bind-key -T copy-mode-vi C-v send -X rectangle-toggle; \
   bind-key -T copy-mode-vi y   send -X copy-pipe-and-cancel 'xclip -selection clipboard -in'"

if-shell -b '[ "$(echo "$TMUX_VERSION >= 2.9" | bc)" = 1 ]' \
   "set -g message-style fg=red,bg=black; \
    set -g message-style bright; \
    set -g window-status-style          fg=default,bg=default; \
    set -g window-status-current-style  fg=default,bg=cyan,bold; \
    set -g window-status-bell-style     fg=red,bg=black; \
    set -g window-status-activity-style fg=white,bg=black"

I raised an issue about the problems with tmux's non-backward-compatibility here. The summary is that the tmux devs will not support backward compatibility, nor will they adopt a version numbering scheme which highlights which versions contain breaking changes. 😢

I also raised an issue to support numeric comparators for %if.