Hi,
No there i no problem if you use it in the IC mode as well as in the OC mode when no action is selected or when selected action will not affect anything. The input logic behaves on the basis of the TCTL3/4 registers setup. Read TCTL3/4 registers and TCTL1/2 registers. I can't see MCU number to be more specific but it is common feature.... you can disable capture in IC mode and action on output pin in OC mode.
Plus, please read more info for
http://www.nxp.com/docs/en/application-note/AN5207.pdf
and
http://www.nxp.com/docs/en/application-note/AN3262.pdf
search for "unused" keyword.
If this does not answer your question(s), or I have forgotten something, or if you need more assistance, please contact me again.
Best Regards, Ladislav