You can possibly use a separate/dedicated receiver (dongle) just for the remote and assign that device to XBMC (i.e, using the regular mouse & keyboard on the second screen, and the 'isolated' dongle to simply receive IR for XBMC), similar to the way you can assign a bluetooth device for one specific purpose. But it has to be invisible to X, of course, so it doesn't grab it. I assume this will have to be done if one wants for use the new Tivo Slide Pro remote, for instance (which has a USB RF, non-bluetooth dongle included.)
btw. - setting focus with wmctrl obviously works but is not really an option IMO, since as soon as one uses the second screen the focus is pulled away. This would assume that the second screen isn't being used (which kind of defeats the purpose of having a multi-head setup in the first place)
As a side note– although the non-SDL XBMC version in the FernetMenta branch supports multi-head properly (vs. the crippled official XBMC branch), there has apparently also been changes made in both the WMs and Xorg in newer Ubuntu releases (>=13.10) which are impacting the multi-head functionality. I did testing on several systems (Ivy Bridge & Haswell) and the only way I found to run XBMC properly on a 13.10 system was in a separate XBMC session (thus defeating multi-head once again). The Fluxbox session, XFCE4, Gnome sessions etc. all failed to use the second display (despite XBMC thinking it did). The Ubuntu session worked, but only in 60Hz, even with all relevant modelines added to the xorg.conf.
(seems there aren't that many who actually run a true multi-head system, since then these changes would be immediately apparent.)
Sorry for the digression.