Setting the Gamerule "commandBlockOutput" to false doesn't affect commands blocks' output as of 13w39a.
Linked issues
is duplicated by 14
MC-32676
/gamerule commandBlockOutput false no longer works
Resolved
MC-32678
Gamerule commandBlockOuput not working
Resolved
MC-32682
CommandBlockOutput isn't working
Resolved
MC-32707
gamerule commandBlockOutput false doesnt work on minecart with Commandblock
Resolved
MC-32713
commandBlockOutput false (not working)
Resolved
9 more links
The only new thing with Command Blocks in 13w39a is a "Minecart with Command Block", don't know if this could be related to the respective gamerule not working ...