Eric, if you're patching digitally within your interface, you're still slaved to the master clock of your device so you wouldn't be able to play back the recording at 24/88.2 and simultaneously record at 16/44.1 in the same box, unless your interface miraculously had two independent, port assignable clocks (not a bad idea really, but would it be good for anything else?!).
I currently interface PT with a Delta 1010 but as soon as I get the cash for a Focusrite ISA 428 I'll take the 1010 out of the chain and make my ProFire 2626 the main interface. I currently don't use the ProFire except for mic pres and outputs to go outboard before going into PT (it doesn't have inserts

). When I get the Focusrite though, I'll have the 4 pres plus the 4 extra inputs for my other outboard pres flying S/MUX into PT with extra ProFire pres if need be.
I think ultimately, some form of mastering software is my solution, but what softwares are out there for this purpose? I know of Wavelab, the former SoundForge (whatever Sony calls it now) and Peak, but Peak is Mac only I believe. Is there anything else? Surely there's more...
Cary