I'm thinking that the simplest and most straightforward solution would be to have an option in SONAR to "lock" the input mappings.  The way it appears to work now is that SONAR "helps you out" by automatically remapping all the inputs to inputs that actually exist.  This is kinda pointless on a live recording where...once it's recorded...you aren't inputting anything else.  All that's left is the mixdown.
 
So...once the mixdown is done and you're happy with all the plugs and settings and stuff...you should be able to strip out all the audio and save it as a template...but now the inputs don't match up.
 
I suppose that, once you have the template fully tweaked (post mixdown), you can then take it back to the board and reassign the inputs...but that's time consuming and (more importantly) error prone if your track and input numbers aren't strictly consecutive.  That falls down when you want to have a stereo track for the keys and another stereo track for the toms...and the wireless mikes are on another page.
 
So...Feature Request..."Input Assignment Freeze"